I wish there was an absolute answer for you, but I'm afraid there isn't. Some security software sees danger where there truly isn't any and falsely labels legitimate programs as being malware. Some security software misses dangerous malware and lets it live on your computer.
Since you've already downloaded and installed the program and cleaned up the trojans (multiple times) I would probably go ahead and try running it since you really need it. I would however strongly recommend you scan again immediately after using it to be sure it doesn't try to sneak the trojans back onto your computer.
It's possible that the program in question is written in such a way that your security software is seeing an issue that truly isn't there, but you just don't know. If the program runs fine, and your future scans show no trouble, then you should be okay. If the program crashes then it's likely the trojans were a necessary part of the program and you'll have to decide if the risk outweighs the reward.
Fly!!! Eagles!!! Fly!!!