Like the above poster said, you could have the problem if you connected the RDS encoder for the side-chain operation, but failed to configure it for side-chain and instead left it in the loop-through mode. The pilot that is sent to RDS for synchronization in that case won't be used for sync at all, but would be passed through to the output and get mixed in the exciter/processor with the MPX signal from the processor (which also contains the pilot). If there are changing phase issues, the two pilot tones would interfere.
The other possibility might be that you have a stereo generator built-in the transmitter, but you failed to turn it off/remove it from circuit. There might not be any audio signals present in the built-in stereo generator, but it would be outputting pilot tone that is probably just summed with the MPX signal coming from your processor. The two signals would most certainly not be in phase, which would cause the pilot to be modulated. I've ran into problem like this before on one radio station where they had the problem of losing stereo and, of course, blamed it on their Omnia. It turned out they had the stereo generator turned on in the exciter.
Regards,
Goran Tomas