In my little sci-fi story I'm writing, my characters use a device similar in design to a smartphone... They simply call it a comm, short for communications. But every grammar app I use to check my writing wants to capitalize it for some reason. To me, comm would be no different than saying car. "He opened the door to his car." "He touched several icons on his comm." So, should it be Comm or comm?
For your use, I would say comm, lower case. When I typed that word just now and then looked it up via my dictionary, it gives it to me as lower case. Perhaps your grammar checker isn't recognizing the abbreviated form of communications and is guessing it's a proper noun that it then wants to capitalize.
No machine grammar checker is ever going to be perfect. There's no reason or rule that I can think of that would make your use of comm something that should be capitalized. It's not a brand or someone's name, nor is it an abbreviation for a formalized position like the Command Center, or something of that nature, which even then is questionable. Definitely lower case.
Yeah, I'd say if you're writing sci-fi get used to ignoring your spell checker. I write in OpenOffice and it even thinks real words like "hysteretical" are misspellings. So of course it doesn't know what to do with made-up alien languages or technobabble. This does mean you have to do a bit more of your own proofreading, but you should really be doing that anyway. A spell checker won't point out that you wrote "Let's eat Grandma!" instead of "Let's eat, Grandma!"