Are you talking about folds or you mean the navigator view? Can you pl. attach a snapshot?

I'm referring to the fold icons near the left margin within the XML editor.

Please attach the xml you're having problems with. It might work me, hence attach a snapshot showing the error.

I did a few more tests and it looks as if you have 2 XML files open, XMLA and XMLB, and XMLA has the focus prior to
closing the IDE, then upon restarting the IDE, the collaps reappear in XMLA but not in XMLB. The reverse is true if
instead XMLB has the focus prior to closing the IDE. So the collaps reappear in the XML upon starting the IDE only if
that XML file had the focus prior to shutting down the IDE, it doesn't reappear in any of the other open XMLs (you have
to reopen them in order to get the collaps). 

Here is one kind of XML I was using, but it makes no difference as long as it well formed:

<?xml version="1.0"?>
<FitnessCenter>
        <Member level="platinum">
                <Name>Jeff</Name>
                <Phone type="home">555-1234</Phone>
                <Phone type="work">555-4321</Phone>
                <FavoriteColor>lightgrey</FavoriteColor>
        </Member>
        <Member level="gold">
                <Name>David</Name>
                <Phone type="home">383-1234</Phone>
                <Phone type="work">383-4321</Phone>
                <FavoriteColor>lightblue</FavoriteColor>
        </Member>
        <Member level="platinum">
                <Name>Roger</Name>
                <Phone type="home">888-1234</Phone>
                <Phone type="work">888-4321</Phone>
                <FavoriteColor>lightyellow</FavoriteColor>
        </Member>
</FitnessCenter>

Sorry, it works for me. Let me repeat, can you please attach a snapshot (picture) of the IDE with the no-collapse view.
Remember, a picture is worth thousand words :).

Created attachment 66108 [details]
Missing XML Collapse Nodes

In the screenshot, the file mappings.xml has the nodes (not visible in the screenshot), but the file test.xml does not
have the nodes. When I closed the IDE, mappings.xml had the focus, which is why it has the nodes upon restarting the IDE.

I am not able to reproduce this issue.  After reopening an xml file the collapse nodes etc near the margin are not there
for about 1 sec but before I can even click in the editor they have appeared.

Product Version: NetBeans IDE Dev (Build 200808010201)
Java: 1.5.0_13; Java HotSpot(TM) Client VM 1.5.0_13-119
System: Mac OS X version 10.5.4 running on i386; MacRoman; en_US (nb)

udeleng, for you does it appear even if you just close the file that does not have them then reopen it without
restarting the ide?

Yes, If I reopen the file or simple type into the file the collapse nodes appear.