Errr wait a moment....are you installing the SH2 1.1 patch or the PA 1.1 patch? You might have been confused, because there is a 1.1 official patch for Sh2 (From UBI) and a 1.1 patch for PA (From us PA Dev team), and both are NOT the same.
I think from your explanation that you are installing in the following order:
-Sh2 from the CD (That is version 1.006 of the original SH2 game)
-1.1 patch for PA
-1.0 version of PA
That would be wrong!!
The first thing you should try is to install just and only the Pacific Aces 1.0 mod. Reserve the patch 1.1 for later, when you are sure 1.0 works well.
The correct order is as follows:
-Clean install of Sh2 from your CD
-SH2 1.1 official patch from Ubisoft (NOT our 1.1 patch for PA!!!!), which you can get here (It's about 22MB and a slow web, be patient):
http://www.silenthunterii.com/intro.html
-PA 1.0 version install (The ~100MB file downloaded from subsim.com)
Please verify you got this all OK
and report if it works.
When you are sure this works, we can try to install on top of that the 1.1 patch for PA.