It may also be worth checking the RCA's (unless you're using the high level inputs
).
I had a similar issue when i first did my stereo install, ended up being the brand new, gold plated, oxygen free blah blah blah RCA's were faulty.
Is it just the splits running off the amp? 4ch bridged to 2 I presume. If you haven't bridged the channels, and you're utilizing the other two channels also, but they're not popping, it would indicate that's it's not an earthing or remote switching issue, rather just an issue related to the channel the splits are on.
Good luck.