As noted in your vim_use thread, I doubt very much that it's a bug in system(). More likely it's a problem with your system path or use of 32-bit calls in a 64-bit application. We can't debug the command unless you tell us what it is.
There were several 7.3 patches in a row (I think in the 400s) handling default shell escaping in Windows. I don't see your Vim version in this thread, do you have those?
If so, what values do you have for the following options?
'shellxquote' (should usually be ( or "()
'shellquote' (should be empty)
'shellslash' (causes problems with shellescape() function when set)
'shellxescape' (should contain ( and ))
'shell' (should be cmd.exe or full path to it)
'shellcmdflag' (should be "/c" or "/c /s" or similar)
I remember parentheses being problematic, but I thought that problem was solved.
See http://vim.wikia.com/wiki/Execute_external_programs_asynchronously_under_Windows#Some_notes_on_cmd.exe_quoting which also has links to the vim_dev discussions on the patches.
If all your options look to be in order, you might be able to manually escape the () characters with '^' but I didn't think you needed to. You might also try "( instead of just ( as a shellxquote value. If neither of those work you can try " but I *know* that has problems in some common situations, which is why ( and "( were introduced.
It sounds like the issue is fixed for this plugin at least. But it sounded like Yegappan was going to bypass the shellquote settings entirely by writing to a script file and running it instead of running the command directly.
If you don't have any further problems it's certainly not worth fighting with Windows cmd.exe.