I don't remember if your anchor locker is one of the models that drains/overflows into the ski locker. If so, that's where I'd start, changing out the drain fitting. I don't recall the year(s) that had that setup.
Plug in, or plug out, when it filled with water? If it was on the water, add it to your checklist to pull the plug and allow it to drain as much as possible. It'll NEVER drain fully thanks to the fitting, but so little should be left, that the heat should dry out most of it, leaving a line after evaporation. I have a big sponge that I use to get out tons of excess both in the ski locker, and the anchor locker. Your anchor locker will never drain fully either, but the mosquitoes can get out through the top openings around the nav lights.
If it was NOT on the water, and the leftover water was from you cleaning out the ski locker, you were likely level, and never had a chance for the water to drain. Dunno what your jack is, but if you've got the ARK, lift it as high as possible and put something underneath that wheel, and make sure it can't roll off. Chock the wheels (both sides, just in case it wants to hokey pokey to the free side), and raise that nose as high as possible. If you don't have an ARK, get a car jack and either build yourself a platform out of bricks, 2x4's, 4x4's, etc and use the jack to raise the nose as high as possible. Next time you're pulling it out at the ramp, plugs out, and linger a bit while everything drains. IIRC, you wet slip - if that's the case, get a battery powered pump if there's too much to sponge
https://www.amazon.com/TeraPump-TRHA01-Battery-Operated-Transfer/dp/B00APU2X0K Remove as much as possible, then sponge out the remaining.
There should be a seal around the lip of your ski locker, albeit a shitty one that will allow some water in, no matter what. See where the gaps are and add/fix/replace. The trough around the outer edge of that seal is supposed to direct everything away from the inside of the ski locker, and out to the deck drain, leading to your scupper, but it's nowhere near as efficient as it needs to be, hence the added seal.
There really is only 3 ways for water to get into your ski locker (4, if you consider wetsuits, skis, boards, etc). Anchor locker overflow, drain plug allowing water in due a bad or non-existent seal under the fitting, and over the top and around the seal due to rain or washing down the deck. Gotta determine how it got in there first, and see what's most likely. If the drain plug has a bad seal or no sealant at all, that never drains fast enough. That drain plug dumps directly into the bilge, and it's large enough that if it is plugged, you should be able to visually see the impediment without much effort, other than getting down in there to eyeball it.
Hope that helps you track down the culprit.