Is your TRiLOGI version 6.2x?
If so, please upgrade your i-TRiLOGI to the latest Version (now shipping 6.31 build 03). You can go to "Help" menu and follow the "TRiLOGI Upgrade" link.
There was an issue with newer multi-core computer in version 6.2x where both CPU cores tried to compile the same program and resulting in strange compilation error (it explains why you received "function already energized" errors). When you transfer program through the TLServer, the two CPU cores are probably processing different threads so the problem did not occur.
By right the O/S and Java JRE should have prevented this from occurring but apparently they didn't (not sure whether it is Windows fault or Java fault). In any case we had to rewrite the part of the program to prevent two threads from calling the same compilation function and this should be resolved in Version 6.3x.