Hey, sorry I didn't get back to your other message. Sometimes I have a lot of time and other times I don't. :-)
The clock signal from the Alesis should be sufficient to keep your loops in sync. There's a little green light on the loop number indicator that should signal the "1" and another green light to the right that shows each clock beat. Perhaps your drum machine's 1 is off. Or, perhaps you're clicking on the loop change too late. This has always worked flawlessly for me but I've never used an actual drum loop. We just use a single click. Though, it's really the same thing. It's just a trivial sequence.
Make sure that you turn the drum machine on after the echoplex is on.
Try clicking the Next Loop button even earlier.