Poker Grapher reads your registry to find the PT DBs (HoldEm, Omaha, & Stud). If PT is functioning correctly and importing hands, then Poker Grapher should find your PT DBs. If you use Vista, make sure both PT and Poker Grapher are both started using the "Run as Administrator" option.
Are you using the latest Poker Grapher Beta,
v1.5.0?
If PT Omaha is working correctly and you're using Poker Grapher v1.5.0, then please run Poker Grapher in debug mode. Go to Start -> All Programs -> Poker Grapher -> Poker Grapher (debug mode). This will create a log file PGLog.txt (usually located at C:\Program Files\Poker Grapher). Then paste the contents of the log file in a PM to me and I will see what I can find.