With a parallel loop, you're only applying it to part of the signal (probably 50%) and the un-EQd signal will still be getting through. My guess is that the signal sounds fatter and fuller with the EQ off when in the loop, because your EQ is filtering out the things that make it sound fat and full in the first place.
Some Markbass amps (for sure, the LM2 and LM3) had an internal jumper that allows you to change the loop from parallel to serial. That means you get the whole signal modified, at the expense of getting complete silence if the effects chain fails.
The other thing to be aware of is that most effects loops are designed to work with line-level voltage equipment (think rack effects) whereas most stomp boxes work at instrument level voltage. So they may not work properly, may require gain changes, or they might be absolutely fine.
And with house amps, not only do you have to worry about whether they have loops, you also have to find out whether they're serial or parallel.
My experience is effects loops on bass amps are best avoided altogether, unless you have something like a rack-mounted DBX 166 studio compressor and want to apply it to the whole signal, all of the time.