using merge script to run few custom compare tool

Hi ,
I am using "External Compare Tools" Preference page -> custom to run batch file  that activate perl scripts .
In the script I analyzing the file extension and according to it run the correct compare tool
e.g
*.cls ,*.sbs will activate Rhapsody Diffmarge tool
*.cpp *.c *.txt etc ' will run "Beyond Compare" compare tool

this script is working fine for "2 Way compare" and it run the correct compare tool.

The issue is with the "3 Way compare"  I can't make it work .
When I am trying to merge file the compare tool dosn't run .
I can see with "Process Explorer " tool that the merge script batch file is running ( but not the perl that activate inside).
I did verify that all arguments are correct by testing it out side Eclipse client RTC tool.
Any  idea what is wrong ? can be that the arguments input for batch script is too long ?

Thank,
Mickey