Reaktor is great stuff, but I continually run into the following problems.

1. With several ensembles, espcially Junatik, whenever I play a pattern from the start with a Junatik patch loaded, the MOD envelope parameters will all reset to 0. I have to uncheck "Activate MIDI In" on the knobs to stop this from happening - VERY annoying. I don't have any sort of screwy MIDI controller set up either, just a simple Edirol PCR-30 -> PC.

2. With several ensembles, most notably Uranus and 3xOsc, I get repeated "Global loop" errors or something along those lines with modules like Counters and Accumulators. I don't remember the exact technical details, but they happen constantly, and I check the "disable global event loops" option.

If I remember,the Junatik mod envelope resetting itself happens when the host sends a controller reset message.I'm not a FL person;does FL have a way to disable sending a reset at the start?Otherwise,you're stuck with what you're doing.
Counters and accumulators will give you event loops if not properly handled.Chris List gave the best fix in the Reaktor forum a day or two ago-check for the thread 4.13 crashes...
ew

audio options -> reset plugin on transport. Try unchecking that. Not sure it's the problem, but worth a try...