Do you still encounter this problem? I'm unable to reproduce with Firefox 11.

Yes, I do. Sometimes the bookmarks will show up, but you can't open any bookmarks items. Sometimes you can open the items but the extension doesn't work. But always I can't open the add-ons page and I need to open the Firefox version from Mozilla and disable the extension to get the Fedora compile of Firefox to work properly. I just tried it with 11.0.

In was setting up my sons computer with a fresh install of Fedora and it does the same thing. That was a 32bit version of Fedora 16

By further investigation I found out PassIFox behave strangely sometimes. After installation installed extensions list is empty. Root of this problem seems to be in extension itself. I also tried official mozilla release for linux: 
ftp://ftp.mozilla.org/pub/firefox/releases/11.0/
and I've encounter same problems. I'll try to look into in further but since this seems to be extension problem we can't do much about it.

I have the same problem. I have freshly installed 32bit version of Fedora 16 and Firefox 11 from fedora repos doesn't work correctly with PassIFox. Official Mozilla build extracted from firefox-11.0.tar.bz2 works flawlessly.
Extension crashes Firefox shipped with fedora then "Rememeber passwords for sites" is checked in preferences. Are there any differences in certificates or anoter encryption stuff?

P.S. In order to get extension working just remove .mozilla from home directory and allow Mozilla's build to recreate it.

I've updated everything to Firefox 12 and some of the issues have been resolved but the extension still doesn't work on the Fedora build, it only works on the Mozilla build. To simplify this I'll go through the steps and the results.

Here is what I did:
1) Remove .mozilla directory;
2) Start Mozilla build Firefox;
3) Select don't import anything;
4) Install https://passifox.appspot.com/passifox.xpi;
5) Restart Firefox;
Doing the above gets me a message from PassIFox to connect with KeePass and after this the addon works flawlessly.

Doing the same thing only with the Fedora build:
1) Remove .mozilla directory;
2) Start Fedora build Firefox;
3) Select don't import anything;
4) Install https://passifox.appspot.com/passifox.xpi;
5) Restart Firefox;
Firefox starts and seems to function correctly, except the addon doesn't function. The only thing that I can see that works is that the addon has added the context menu item "Fill User & Pass" when right clicking a login input but selecting the item does nothing. The old issues with the addon page not opening and the bookmarks menu not functioning have disappeared.

Thanks.

Do you see any errors in debug console in the fedora build? (tools -> web developer -> error console)

Yes, there are. I redid the steps from 1 to 5 from above with the Fedora build and here are all the errors I get.

After step 3:
Timestamp: 04/05/12 10:50:25 AM
Error: profiles is null
Source File: resource:///components/FirefoxProfileMigrator.js
Line: 372

After step 5:
Timestamp: 04/05/12 10:51:59 AM
Error: uncaught exception: [Exception... "Component returned failure code: 0x80570015 (NS_ERROR_XPC_CI_RETURNED_FAILURE) [nsIJSCID.createInstance]"  nsresult: "0x80570015 (NS_ERROR_XPC_CI_RETURNED_FAILURE)"  location: "JS frame :: resource:///components/nsLoginManager.js :: <TOP_LEVEL> :: line 95"  data: no]

Timestamp: 04/05/12 10:51:59 AM
Error: uncaught exception: [Exception... "Component returned failure code: 0x80520012 (NS_ERROR_FILE_NOT_FOUND) [nsIXPCComponents_Utils.import]"  nsresult: "0x80520012 (NS_ERROR_FILE_NOT_FOUND)"  location: "JS frame :: resource://passifox/modules/KeePassFox.jsm :: <TOP_LEVEL> :: line 7"  data: no]

After going to my financial login website:
Timestamp: 04/05/12 10:53:22 AM
Error: uncaught exception: [Exception... "Component returned failure code: 0x80570015 (NS_ERROR_XPC_CI_RETURNED_FAILURE) [nsIJSCID.createInstance]"  nsresult: "0x80570015 (NS_ERROR_XPC_CI_RETURNED_FAILURE)"  location: "JS frame :: resource:///components/nsLoginManager.js :: <TOP_LEVEL> :: line 95"  data: no]

Timestamp: 04/05/12 10:53:22 AM
Error: tipElement is null
Source File: chrome://browser/content/browser.js
Line: 6508

Timestamp: 04/05/12 10:53:23 AM
Error: uncaught exception: [Exception... "Component returned failure code: 0x80570015 (NS_ERROR_XPC_CI_RETURNED_FAILURE) [nsIJSCID.createInstance]"  nsresult: "0x80570015 (NS_ERROR_XPC_CI_RETURNED_FAILURE)"  location: "JS frame :: resource:///components/nsLoginManager.js :: <TOP_LEVEL> :: line 95"  data: no]

After selecting "Fill User & Pass" from context menu:
Timestamp: 04/05/12 10:54:39 AM
Error: uncaught exception: [Exception... "Component returned failure code: 0x80570016 (NS_ERROR_XPC_GS_RETURNED_FAILURE) [nsIJSCID.getService]"  nsresult: "0x80570016 (NS_ERROR_XPC_GS_RETURNED_FAILURE)"  location: "JS frame :: resource://gre/modules/XPCOMUtils.jsm :: XPCU_serviceLambda :: line 232"  data: no]

I just checked and with the Mozilla build there are NO errors in the error console when doing steps 1 to 5 from the post above.

Yes, you're right, I can reproduce it.

Looks like the firefox/xulrunner split is a problem here.

From the debug information you had me provide I was able to find the solution. It seems that the extensions uses:
resource://gre/modules/services-crypto/WeaveCrypto.js

By changing it to use:
resource://services-crypto/WeaveCrypto.js

The plugin now works.

Thanks.

Ahh, I see. Please report that to the extension authors then. Thanks!