It's been 19 years, and I'm still trying to figure out why the VOY writers did this, since it was such a contrived thing. The only logic I could come up with was that Beltran was getting a paycheck for doing essentially nothing, nobody knew what to do with the Chakotay character, and they decided to stick Seven with some guy for some reason but every other male character was an illogical choice. (Well, Chakotay was an illogical choice too, being old enough to be her father and that they had zero chemistry or even interaction for the entire series.) So they wrote some scenes for Chuckles so he could actually do some work, but they essentially made him a creepy old man.
Either that, or the writers were just smoking a lot of weed.