In a way it seems to be a permission problem.  This is the error I got
(Firefox 2.0.0.3 on Edgy):

Error: [Exception... "Component returned failure code: 0xc1f30001 
(NS_ERROR_NOT_INITIALIZED) [nsIMIMEInfo.primaryExtension]" nsresult: 
"0xc1f30001 (NS_ERROR_NOT_INITIALIZED)" location: "JS frame :: 
file:///usr/lib/firefox/components/nsHelperAppDlg.js :: anonymous :: line 238" 
data: no]
Source File: file:///usr/lib/firefox/components/nsHelperAppDlg.js
Line: 238

I dont know if this message is equivalent to the NS_ERROR_FILE_ACCESS_DENIED 
error getaceres got in 
https://bugs.launchpad.net/ubuntu/+source/firefox/+bug/65164/comments/2, since 
he used an earlier Version of Firefox.
As it says the error is related to this piece of code in nsHelperAppdlg.js:

if (aLocalFile.isExecutable() && !this.mLauncher.targetFile.isExecutable()) {   
  
        var f = aLocalFile.clone();
        aLocalFile.leafName = aLocalFile.leafName + "." + 
this.mLauncher.MIMEInfo.primaryExtension; 
        
        f.remove(false);
        this.makeFileUnique(aLocalFile);
}

I dont quiet get the semantics of this paragraph (for example what the 
differnce between the two Files is and why they delete the first one), so a 
cannot say if its a bug or a feature ;).
As soon as the Fat32 partition is mounted with permissions rwx on files and 
directories, aLocalFile is always excecutable. When downloading a regular file 
(something not a binary executable), Firefox seems to set the mode of 
targetFile to 600, so
the expression is true and I get a aborted download and a 0 byte file.
Watching the network traffic revealed, that Firfox starts donwloading as soon 
as I left click on a link; seems it is prefetching the download while the user 
selects the destination. As soon as I click Ok the download stops.
Right click -> Save target as... works nicely, as nothing is prefetched and the 
section in nsHelperAppdlg.js is not executed, but this procedure is not 
possible for all downloads.

This leads to two workarounds for this problem:
1. Quick and dirty commenting out the above section in nsHelperAppdlg.js. This 
is not a good idea as long as the meaning of it is unclear, even though I 
discovered no side effects.
2. Mount the partition with separate dmask and fmask (for example 
dmask=007,fmask=117). As long as you dont need to execute files on that 
partition, this is a much cleaner solution than the first.

Of course these are just workarounds, so a real fix still needs to be
done.

-- 
Firefox 2 can't save to fat32 partition
https://bugs.launchpad.net/bugs/65164
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