Are you the webmaster/developer?

One thing I noticed is that many spans have "clear:both" which can force them lower than intended (i.e., they might only need clear:left or clear:right).

There are some other problems with the tags in the page that may be causing unexpected results. You might want to try the W3C validator to help in developing a list of issues to address: The W3C Markup Validation Service. It can be pretty ugly the first time, so you might first want to take a scan through the code and add in the missing quotation marks for attribute values, and address other obvious XHTML requirements.

You are trying to place a block element (DIV) in a SPAN and that doesn't work, so the span is closed and a DIV is opened in current Firefox version. Older Firefox versions probably ignored the DIV.

You can see that part of the code as red text in the page source.
You can select the text and use View > Selection Source to see what Firefox makes of it.

<span >
<div align=center>
<b><u><font size=2 face="Verdana, sans-serif">
What Is ...
</font></u></b>
</div>
<p align=justify style="margin-bottom: 0in">
<font size=2 face="Verdana, sans-serif">
<B>Targum Onkelos:</B> An early (1<sup><small>st</small></sup>-2<sup><small>nd</small></sup> Century CE) translation/paraphrase of the Torah into Aramaic; attributed to a Roman convert to Judaism, Onkelos; used in Babylonian synagogues during the Talmudic era
</font>
<br>
</p>
</span>Targum Onkelos seems to agree, translating this word as
"excrements".
</p>
<p align=justify style="text-indent: .25in">
The <span style="float: right; clear: both; width: 2.6in; border: 1px solid #000000; padding: 0.06in 0.11in;
margin-left: 0.1in; text-indent: 0in;
margin-top: 0.1in; margin-bottom: 0.1in; background: #ffffa0">
<div align=center>
<b><u><font size=2 face="Verdana, sans-serif">
Who Is ...
</font></u></b>
</div>
<p align=justify style="margin-bottom: 0in">
<font size=2 face="Verdana, sans-serif">
<B>The Rashbam:</B> Rabbi Samuel ben Asher (1085-1174), a grandson of Rashi; lived in Northern France; worked from the plain meaning of the Hebrew text even when this contradicted established rabbinic interpretaton
</font>
<br>
</p>
</span>

> Are you the webmaster/developer?

Guilty as charged.

I've run it through the W3C validator as you suggested and have made a number of changes - the error count has gone down from 320+ to about 32. Some may take a little more time to fix. Since all the HTML code is actually in m4 files and the individual pages are largely macro calls and plain text, the roll-out is fairly painless across 450 pages. However (see my second reply), the problem hasn't completely cleared ...

BTW, why does Firefox have the symbol   in red in Tools->WebDeveloper->PageSource? It does for same for ©

OK, so I have taken out DIV inside SPAN and the result, as you'll see is now quite a lot better. At least all the text is now inside the boxes. However, in doing that I have lost one (relatively) important formatting feature - centering the title line of each box.

You'll see that now ...

  http://www.messianictrust.org.uk/parashiyot/vayikra-9.htm

although I have arranged two inner SPANs to hold the two pieces of text - heading and body - the heading is (incorrectly) left-aligned, while the body is (correctly) justified. Why has it obeyed one style and not the other?

  <SPAN STYLE="TEXT-ALIGN: CENTER">

as opposed to

  <SPAN STYLE="TEXT-ALIGN: JUSTIFY">