Your average healthy man tries to masturbate 4 to 6 times a day, but can only usually find time and privacy to get away with this solitary recreational thrill maybe twice a day.
That's a conservative estimate for a male surrounded by millions of human beings with extensive distracting duties and obligations.
I think it's safe to say that Chakotay had free and unrestricted reign of his personal space if Kathryn was so busy with her monkey that she failed to notice him landscaping and building a spa resort under her very pretty little nose.
So he probably masturbated almost 400 times during their 60 day vacation from Voyager.
The logical conclusions of this supposition...
a. Chakotay didn't have the energy left to pursue her, what with all his needs being satisfied, that what she had to offer was redundant because of his intensive affection self supplied.
b. If there's anything a thousand shows called CSI have taught us is that as she was living inbetween hundreds of overlapping "crime scenes" that she must have noticed some evidence of his hobby, but pretended not to understand, and that it was this monster sized denial which grew into the most encompassing iron curtain that is the real reason she spent so much time with her monkey. Cause and effect.
c. Kathryn's ability to not think about him like that was absolute, so it's just precious that she didn't understand the mystery of the 1001 vanishing hand towels.
d. Whether he was aware or not, Kathryn kept catching him in the act. Was he careless, or was it an even clumsier invitation to participate than the Angry warrior Speech? In either case he was an idiot and if she had to spend her time with some bloke who can't stop touching himself, she picked the monkey.
e. She was frightened, that if he did that to himself 200 times a month then she might have to have that be done to herself 200 times a month, and she just wasn't prepared for that sort of stress on her middle extremities after opting for the last two years to cross her legs and wait for Mark.
f. What was he using as a mental aid? Did he have PADD porn, or a healthy imagination stocked by a wankbank clearly in the black? In one case he was cheating on her with many other women, or one special lady he was obsessed with, who was probably most certainly her, although not the "real" her, which was intellectual property theft at best and rape by proxy at worst, neither action of which is worth rewarding with an adult relationship.
G. His peyote machine that creates a borglike hive mind where they can have lucid dreams in completely program-able environments is without a doubt a knocking shop by another name, but for "spiritual" reasons, no matter how many spirit guides he nails (Furries represent?), Chakotay wouldn't let her abuse/debase this religious artefact with her own thoughts on romance and release, which is if you think about it a sort of ransom by a sort of emotional terrorist. Only a fool negotiates with terrorists. (If the saftey protocols on a Federation replicator won't produce "chocolate" I think it's highly unlikely that she fabricate her own peyote machine in the camp on New Earth, if she didn't think to mock one up before leaving Voyager.) he had her over a barrel and she doesn't like bullies. She'd eventually beat him into a coma to get that peyote machine because she is a good person who he should share his possessions with
h. She can smell the sex on him. The constant odour permeating off his pants must make the lady roll her eyes and yawn about how predictable and simple men are, that there's no way that she could respect him enough to take him on as a lover if he can't escape perpetuating a farcical caricature.
i. In all likely hood, she was rubbing one out as often and as skilfully as he was on the the opposite side of the camp. They probably subconsciously worked out a scheduling rotor to clockworkilly avoid accidents, but if "point A" was that he was too buggered, then "point G" is that she was just as buggered. They were double buggered. (Buggered just means tired. It's a homonym.)
j. Janeway didn't want to ruin it for him? Really after a night with his dream girl, how is he supposed to go back to playing with his monkey? That's just rude. Besides he'd be chemically dependant on himself and any attempt to reacclimatize his metabolism for just and only relationship-sex might kill him if he comes down too cold turkey. She probably likes him too much as a friend to break him like that.