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Example: LangRef / LexAnalysis / Identifiers
Green-shaded grammar section has 3 lines, 2 very long:
identifier ::= id_start id_continue*
id_start ::= <all characters in general categories Lu, ...
id_continue ::= <all characters in id_start, plus character ...
so both online html and winhelp versions have a horizontal scroll bar
underneath.
The 3.0.1 Windows Help version only displays 2 lines and adds a mini
vertical scroll bar at the far right to see the third. If possible, it
would be better if it simply displayed 3 lines like the html version.
Experimentation indicates the following for all the green boxes: if the
type size is increased or the window narrowed so that a horizontal
scroll bar is needed, html (at least as rendered by FireFox) adds it
*underneath* the green box, while Winhelp adds it *in* the green box,
taking up one line and thus hiding the last line of text, thus requiring
a vertical scroll to see that line, which then hides the top line (ugh).
Assuming that there is no configuration option or formatting directive
that can be put in the file to tell winhelp to act differently, a
partial fix would be to add an extra blank line, if possible, to every
green box on conversion to the winhelp version so that all lines would
be visible even when an (now irrelevant) vscroll appears.

It's probably better to split long lines (at 80 chars?) than adding an
empty line in every box. Scrolling horizontally is annoying enough even
without the problem you mentioned.
I don't know if it's possible to split grammar lines like
id_start/id_continue[1], but in this specific case is probably better to
keep the definitions short and explain it further in the following
paragraph.
I don't have any idea about how Windows Help works, but if it uses
something like CSS, some extra padding at bottom could solve the problem
without having to add an empty line.
[1]: http://docs.python.org/3.1/reference/lexical_analysis.html#identifiers 

The lines in the green box do not have to be long in an absolute sense,
just longer than the current window width allows. As soon as the the
window is narrow enough to require a horizontal scroll bar, a vertical
scroll bar is added too because the horizonal scroll bar is added into
the box on top of where the bottom margin and part of the last line was.
I just discovered that if the vertical scroll bar is exactly centered,
everything is visible because the horizontal bar is a bit under twice
the width of the top and bottom margins. If only it started there...

That's why I think that the Windows Help problem still need to be fixed,
but limiting the length of the lines is a good idea regardless of this,
since having long lines and horizontal scroll bars is annoying on the
browser too.
Is the Windows Help python31.chm?
I installed Python 3.1 on Windows XP and tried to open that section.
Here the width of the page depends on the longest line, so the whole
page is large enough to contain both id_start and id_continue (however,
even if this long lines go over the right limit of the page, all the
other lines fit in the visible part of the page). There are no
scrollbars inside the green box, just "global" scrollbars for the page

WinXP, updated, Py3.1.
Start / Programs / Python3.1 / Python Docs
I presume this uses .chm file.
I most definitely have scrollbars covering text in green box.
See screenshot for what I see.

This is what I see here (see attached image). The only scrollbar is the
one at the bottom for the whole page. The file is under Start ->
Programs -> Python 3.1 -> Python Manuals, and the path/file is
C:\Programs\Python31\Doc\python31.chm (you can see it right-clicking on
it from start menu and selecting properties).
I'm using WinXP SP2, the versions of the HTML Help Components are:
HHCTRL.OCX 5.02.3790.2453
ITSS.DLL 5.02.3790.2453
ITIRCL.DLL 5.02.3790.2453
HHA.DLL 4.74.8702.0
Compiled with HHA Version 4.74.8702
You can find this information right-clicking on WinHelp in the
application bar (or on the small icon on the left of the title bar) and
then on "Version...". Maybe you are running an older (or newer) version
of WinHelp.
Tomorrow I'll check with some other Windows.

Same path to python31.chm.
I presume color difference is due to difference selections in
Display Properties / Appearance tab.
When I left- or right-click on upper-left icon as depicted in screen
capture, choices are move, resize, ...., close, About HTML Help. No
Versions. Result of selecting last is popup window
About Microsoft HTML Help. 
Html Help Control Version 5.2.3790.4110
Copyright blah blah
Ditto for right-click on entry in task bar as bottom of screen.
Other programs use the same control.
We are obviously running different 'help' programs. WinHelp versus HTML
Help? I wonder if it has anything to do with vendor customization. My XP
Home is from HP. However, wife's machine from Dell with XP Pro uses the
same version of same control for help with various programs also.
My machine does have winhelp.exe (with pure ? icon instead of ? and
page) and winhelp32.exe (with ? on book cover icon), but they are not
listed in programs / accessories. Latter does not recognize python31.chm
as a help file. The former looks for .hlp files.

I uploaded a few more screenshots.
I was able to reproduce the issue on Vista with HTML Help Version 6.0
and on Windows 2003 Server whit HTML Help Control Version 5.2.3790.3959.
I also tried on another Windows XP SP2 machine with HTML Help Control
Version 5.2.3790.1194 but the scrollbar wasn't there, so I guess they
changed something between .1194 and .3959
The version I'm running at home is probably even older (4.74?) and the
problem seems to affect only the newer versions.

Is this still an issue?

Yes. On win 7, html help control 6.1, the horizontal scroll bar is still put in or on top of the box, but it is thinner so it only cuts off half of the bottom line instead of hiding it completely. There is no longer a vertical scroll bar, which means one can only expose the rest of the bottom line by maximizing the window and shrinking the type size.
This is no an issue for me now because I recently got a 27' monitor with 2560x1440 resolution, so with full screen and still readable type, I can see even the long lines discussed here without a scrollbar. But this will not be true for most. On a small enough screen, I might need a magnifier.
I checked and Internet Explorer works like FireFox, adding the scrollbar beneath the box (or expanding the box to accommodate it).
I just confirmed that the start menu shortcut does the same as double clicking python34/Doc/python34a3.chm. Same behavior. The icon is question mark partly over page.