I know, complete n00b here, so forgive me if this isn't helpful...
You can change the following key in "HKEY_CURRENT_USER\Software\HTC\Manila" and that will make the programs tab show up.
From:
Manila://programs.page.hidden=0
To:
Manila://programs.page.hidden=1
But the issue you state above still happens (At first the softkeys are right, but if you go to the programs tab, it makes all the soft keys change to "All Programs" and "Remove" until you reset).
Installing the two files from post #3184 worked for me though. If you install the "Regular Start Menu + Programs Tab.cab first, let it reboot, then install the "hide program tab.cab" (Which actually un-hides the tab) it works. It also gives you 4 rows of buttons instead of 3.
The first cab actually replaces 3 manila files:
6be6fd25_manila
291a6623_manila
22bb3b19_manila
The second only changes the registry key setting I mention above (the first cab changes this key as well, making it hidden, so you have to do the second one after the first, or just change the key manually yourself).
I'm assuming one of the manila files above is messed up in this release, and that is why installing this fix works. From post #3230 it sounds like the bad file is 22bb3b19_manila, but I haven't confirmed this.
Also, I'm pretty sure just changing the registry entry above worked in the 090328H build without the file change.
[man you guys are too fast... I've had to re-write this post 3 times as more and more info came out
]