We'll see if this process has been improved in WebSphere Portal 6.1, when it will be out and I will get the opportunity to play with it.
So, turns out that you'd be better applying e-fixes by hand, manually, one by one, from the command line. Forget the Java Wizard of UpdateInstaller for Portal, and forget the fix-packs, for instance the installing script for fix-pack 126.96.36.199 which is supposed to apply about 100 patches does not get the job done, properly. This is because fix-pack is trying to start/stop/start/stop the Portal itself several times and probably it gets something wrong on the way.
As such, load yourself with patience, plan for 2 man/day effort and proceed as following:
1. Get all your fixes from Fix Central site. Usually, if using IBM's DownloadDirector, you'll have several zip files downloaded on your folder.
2. Get the Portal UpdateInstaller, unzip it and place it under
3. Create your fix folder as in d:\ibm\WebSphere\PortalServer\fix
4. Then, do the following: read each of the fixpack readme :) Yes, really, do that :) Because some have other fixes as required for successful installation, then you might need to run for certain fixes commands like 'WPSconfig.bat apply-pk35496'
5. So, if you decide to apply a fix, copy its jar file into the d:\ibm\WebSphere\PortalServer\fix folder.
6. Decide how many fixes you want to apply, copy their jar files into the fix folder, making sure required other fixes are already applied or installed in the same run of UpdateInstaller.bat
7. The command line to apply a set of fixes is, from the UpdateInstaller folder, as seen below:
D:\ibm\WebSphere\PortalServer\UpdateInstaller>updatePortal.bat -install -installDir "d:\ibm\WebSphere\PortalServer" -fix -fixDir "d:\ibm\WebSphere\PortalServer\fix" -fixes PK35276 PK37018 PK32211 PK32501 PK32562 PK32570 PK32573 PK32626 PK33082 PK33379 PK33783 PK34220 PK34611 PK34624 PK34828 PK35170 PK35496
Happy patching :)