YES, I have this issue. I never got a good answer on it in this forum in the past. When engaging the EFX loop there is a subtle increase in volume, maybe 1-3 dB? Not so much as you describe but noticeable to me for sure. When gigging I like to use the Mark footswitch to turn the loop on/off so I don't have to work the loop pedals individually. I've never had anyone comment on it but I do notice the ever so slight increase in output volume. To me it seems that there must be a slight level mis-match between what the EFX loop sends to the power tubes vs. what the pre-amp alone sends. To verify it is not a pedal in the loop I've put a 12" cable between SEND and RETURN and the level mismatch is still present.
Not sure what causes the level increase but probably a result of having analogue components where each one is a bit different amp to amp. So, it would make sense that some Mark V's have a more noticeable level increase than others. If I ever send in the amp to Mesa factory for service or a good tune up (Mark is now 10 years old and a bit road worn) I'll ask them to evaluate/comment on this.
Question: did you actually measure the dB increase? If so, how? Just with a voltmeter RMS and then you calculated it? My numbers above are just just ballparked based on my ears.