Hi sorry to hear of this issue! MyDMX 3 doesn't have a hard value limit but the more you do on it the more your computer needs to be able to handle all it is doing. but even the developers themselves say this program was not designed for shows with hundreds of cues set to precise time code/timing.
If you send me your file by way of file send or dropbox, i can have it looked at and maybe fixed, but no promises.
jamesk@adj.com