MS Word suggests question mark, i don't understand why

[msleiners]

I have written following sentence

After all of the computer code have run all result files are collected and put into agreed location

MS Word advises me to put the question mark at the end of the sentence, so naturally i started to wonder whether this sentence sounds ok?

[bhaisahab]

I have written following sentence

After all of the computer codes have been run, all the resulting files are collected and put into the agreed location.

MS Word advises me to put the question mark at the end of the sentence, so naturally i started to wonder whether this sentence sounds ok?

I have marked my suggestions for improving the sentence in red. These are only suggestions because it is not completely clear what you want to say.
I don't know if this will correct your MS word problem, but it isn't a question.