When you decompile it and get that, it's showing you the offsets used. The changes in how the script looks make absolutely no difference on the effects of your script. I don't see a reason why the givepokemon command would be disappearing, make sure you're setting it up as givepokemon 0x(species) 0x(level) 0x(item) 0x0 0x0 0x0, with the species, level, and item values in hex, of course.
EDIT: I just noticed an important flaw, you're missing a parameter on your msgbox commands. It should go msgbox (offset) (msg type), meaning for a yes/no question msgbox @offset 0x5, and for a normal one, msgbox @offset 0x6. Callstd is no longer used (so make sure you have the latest version of XSE). Remove that part entirely, and add msgbox types to your msgbox commands.
One more thing I just noticed, you forgot to start the script with a lock command.
No offense, but your script is a bit of a mess. I rewrote it for you, try this:
Try looking at how that's written and it should help you out.