The obvious questions that spring to mind are:
Is it and the rest of your equipment well grounded, with a separate wires going to a common bus bar, that includes the transmitter and all your other equipment?
When you say you bypass the 998, is that switching into bypass or physically removing it from your system?
I have an MFJ 998, but have not installed it into my system yet, (currently using an MFJ 962 manual tuner) so will be interested in what you find out when you resolve the problem.?
Hope you find that it is something simple to fix and not an inherent design problem.
--
Jeff - NZ2S
JeffBanke