If anything, I would have expected it to be the other way round. If you omit the renderScene()-call, the draw()-call actually triggers some additional calculations that had to be done per frame but are usually done in renderScene(). These calculations were done too early to take a modified plane into account. However, I'm not sure why this should explain the behaviour that you are describing.
Anyway, I've updated the beta-jar of jPCT-AE. Please give it a try and see if that helps. If it doesn't (or makes things worse), can you please provide me with a test case?