ipa,
I have these strobe panels as well, along with other Chauvet products.
The problem isn't really with MyDmx, but rather with the way Chauvet designed how their panels work. You are basically selecting a preset on the fixture that tells it how fast to strobe. DMX is not really controlling the actual strobe. The panels are most likely strobing at the interval you specified, but the start time of the strobe is different. I don't think the fixtures are resetting the start time of the internal clock timer when a dmx command is received (in other words, the internal clocks aren't synced between the fixtures). Syncing lights with precision is best done with master/slave operation in which case only the internal clock of the master is used. There are so many times I wish my fixtures could work in both master/slave mode as well as DMX mode at the same time, in which case they would need a DMX In/Out and a Slave out (kind of like what the colorstrips have).
For example, I have the Intimidator Spot 150s. If I send the DMX command for them to run Preset 2, they are never exactly quite in sync even though they are running the same macro. When I sent the command, one fixture might have been pointing left while the other was pointing down. How do the two know when to sync up together to being preset 2? Unfortunately, without master/slave operation, it's impossible for them to talk to each other and know. In master/slave operation, this works perfectly. Unfortunately, because of the way they were manufactured, when in Master/Slave operation, they only operate in stand-alone mode so I can't use them in my DMX chain and send them commands.
I hope this helps you understand more of what is actually going on. If you want these to be perfectly in sync, you'd have to do what Dj Access said. But I agree with you, MyDmx's lack of layering really sucks.