I've recently acquired a BVP5500. Sounds really nice, however I'm experiencing an issue when used with my distortion pedal, a DigiTech XBD Bass Driver.
Basically, the effect pedal has very little effect! I was using a Peavey combi previous to getting my own amp, so it's not an issue with the pedal itself. (Also using power adapter not a battery).
Level works (as expected), and the morph setting when turned up high has _some_ effect on the sound (though not as much as previously) , tone and blend changes don't have a noticable effect, and there's hardly any distortion in the sound. It's almost as if the amp is filtering the distortion out.
I got another cable and placed the pedal in the effects loop at the back instead of between bass and amp, but this did not appear to make a difference. I've also played around abit with the gain/valve driive and EQ settings.
Based on the observations you expressed here there is nothing that indicates that your BPV5500 is causing your issue.
I will tell you with certainty that there is nothing in the BPV5500 that can "filter out the distortion" as it just plays whatever goes in the input. If you aren't getting distortion from your pedal when plugging in the front input or when using the FX Loop in the back of the amp then it's more likely that something is wrong with either your distortion pedal settings, the cables you are using or your bass guitar volume.