You misunderstood my question. Why don't you start convert.exe from a batch file (not "manually") with a line like this...
start "C:\Program Files\Convert\Convert.exe"
That is, start followed by a space then the program drive letter, path, and filename (all in quotes because of the space in 'Program Files')
Have you tried this?
The /d switch changes to the directory that is named; you would do this if you wanted to actually be in that directory for some reason. If you did not need that specifically, you would use the form that I described above.