Hi Actman,
I've had this exact problem you're describing on both jukeboxes I attempted to install the Wireless IR Control kit. After a little research I found that Rowe did release an IR Remote Ground Adapter that resolved this issue (kit #21963901).
The description on the installation instructions:
"When using the infrared remote control on a CD phonograph, an additional ground wire may need to be added to avoid volume fluctuations."
I purchased this adapter, but it's pretty easy to make at home. Basically you run a wire from pin 6 on P3 on the IR Remote Interface to the "common" terminal on the output transformer assembly.
If you want give me your email and I can send you a PDF of the instructions. Hope that resolves your issue.