The only time I've ever managed to cause problems with normal box operation is when there is a lot of hard disk activity. Recording two HD programmes whilst playing back a third is pretty hard on the disk so if something else disk intensive comes along then it can cause these symptoms.
The odd thing is that RS doesn't do anything CPU, memory or disk intensive apart from once a day when it does a complete disk content scan. That's done a few minutes after the box boots for the first time each day so usually occurs during the 04:30 update check. Otherwise RS is very lightweight.
For anyone having pixelation problems, I'd suggest uninstalling everything - all packages - that you can and see if the problem still occurs, then you can reintroduce packages to try and pinpoint the issue.
The problem I have is that I don't see this problem and, as you can imagine, my box runs a fair amount of extra things.
By itself, with no additional packages, the custom firmware shouldn't increase the load on the box measurably so I would be interested to hear of anyone for whom just installing it causes problems.