Most likely the problem is that your PC is not setup to run java programs such as the one PT uses to calculate the winning percentages.
MAKE SURE PT IS NOT RUNNING.
If you are using any version of Windows other than Windows 2000, download and install this file: http://www.pokertracker3.com/products/P ... sjavwu.exe
If you are using Windows 2000 with service pack 4 download and install this file: http://www.pokertracker3.com/products/P ... 2k_sp4.exe
If you are using Windows 2000 with service pack 2 or 3 download and install this file: http://www.pokertracker3.com/products/P ... p2_sp3.exe
Once you have done this, download this file: http://www.pokertracker3.com/products/P ... winpct.exe
It's a self-extracting zip and then run it - it will load 3 files to your PT folder (c:\program files\poker tracker v2). If you have installed PT in a different folder, you'll have to tell it the correct folder to install the files in.
Then go to the PT folder (using Windows Explorer) and find the file regbat.bat and double-click on it. A command window will pop up and close real fast. After this happen, go into PT and see if it corrected the problem.