Andrew, I'm away and on a hotel pc so I don't have the POF File, but I know ZOB has moree squawks than that. CLE TRACON has codes starting with "0". I am sure because it is a problem using TWR Trainer.
Make sure your students have the PRIM option checked when using Sweatbox. The POF file won't be effective without the PRIM. If PRIM is unchecked, VRC will issue 1000, 1001, 1002, etc. Other than that there is no explanation as to why TWRTrainer would affect your squawk codes.
The only way the PRIMing could potentially cause interference with the real-time (USA-W2, S3, EUROPE-CE, etc.) is if the voice channel is set to that of the real-time position. In ZDV I implemented a policy which required Sweatbox students and instructors to change their voice channels to XXX_YY_XXX, where YY was their controller initials. This prevented two controllers (one on Sweatbox, one on the real-time server) to be using the same channel, and it therefore prevents interference.
The VATUSA squawk codes allocated to each ARTCC are the ones that are supposed to be in use. You'll know when someone is using your squawk codes when the CODE error appears in aircraft datatags. In ZDV there are airports without a realistic set of squawk codes because of this document, but because of the limitations of the network, they are required.