For clerics, the maual reads that the number of skill points they get per level is 2+int modifier. My cleric, with 11 int (modifier = 0) only gets one skill point when he levels up. This has been going on for quite a few levels. Is this a typo in the manual, a bug, or what? Any help would be appreciated.

Yes, clerics get 2 + int modifier skill points per level. But the int factor is dependent on your base intelligence only. So I suspect you have 8-9 base int, which gives a -1 modifier so you get 1 skill points per level.
Wearing an int enhancing item won't matter for skill points earned.

If this doesn't apply to you, then it definitely is an annoying bug. But the strengh of the cleric isn't in his/her skills anyway :)