Jamal,
The key is to always keep ignition components and RX components separated. As you have now found that out simply by separating the 2 battery packs. It is a good idea to ALWAYS keep these components as far from one another as possible. However, for future reference, you can get them as close as 6" with great reliability. ALWAYS do lots of testing to be sure. Any airplane should be able to work with FM. If you can get good results with FM, there is almost no reason to switch to PCM.

Jeff C