As stated above,
interference from other masts in the marina is probably the culprit. This happens frequently with my extrenal WI-FI Antenna and to a lesser amount with my VHF in really crowded
marinas.
Just out of curiousity.... Did you try all ten
weather channels and if so, confirming you receive nothing on any of them?
Also, remember that VHF antennas are pretty much line of sight... While sitting in your
cockpit, 6 feet off the
water, you may have a clear line to the broadcasting antenna, but might not from the top of you mast 40 or 50 feet off the
water....
The true test would be hold the hanbdheld at the same height of your mast antenna and see if you get any reception up there...
As far as SWR, yes that could be a problem, but not for this type of intermitent reception.