When you say the filtering has been "beefed up", what does that mean? Any old filters in the amp should be replaced. And it's possible that increasing filter value will help too.
Grounding can have an effect too. If your amp uses a "can" type filter with a common ground you may need to retrofit individual caps so that their grounds can be seperated.
It's also possible that when the filters were "beefed up" that some shinnanigans omitted a ground or filter for the power supply. The amp should brobably be returned to stock working order with known good parts before any further assesment.