When you're using the bootloader, make sure you have DEFINE LOADER_USED 1 at the top of your code. The syntax must be exact and in CAPITAL letters, unless, yes it may give you some weird results.
Now, did you tried with a simple led Blink?
Does the Bootloader return any error messages?
Did you use the same schematic as stated in the MCS help-file?
Are you using Mecanique bootloader or another one?
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