It may not have been the slight parallel signal that caused your problem. Mesa amps have high output impedance in their loops, and if your effect box did not have super-high (1Meg Ohm or more) input impedance, it wil cause tone loss due to impedance mismatch filtering. Adding a buffer will fix that.
Also, if the EQ block was either digital, or routed after a digital processor, the latency could have caused comb-filter artifacts.
An analog EQ with high input impedance (like a GE-7) should work just fine in the loop. It's not the best quality EQ out there, but a lot of the high performance rack EQ units are designed for line-level, so they do not buffer the input signal, which is absolutely required for most tube amps.
The parallel path also depends on your volume setting. There is a bleed path that has nothing to do with the loop. One of the preamp tubes has one chanel working pre-loop, and the other channel post-loop, so there is crosstalk in parallel with the loop. Even if the loop were 100% parallel, this would make it not 100% parallel. The crosstalk is at a fixed level, not affected by the master volume. At high master volume settings, the bleed path is swamped out by the main path. AT very low master volumes (like what you'd use at home), it's very noticeable. The cure is to turn up the master volume.