I had the same thing happen after a rainstorm in 100 degree heat here in AZ. The black cover (from MasterCraft no less) bled dye all over my back v-drive cover and made it a light pinkish color.
I believe that being out in the sun did the best to bleach the color off, but it will probably take a long time and I got too impatient for that.
Give Starbrite Vinyl Cleaner and Conditioner a try:
http://www.wakeworld.com/MB/Discus/messages/65921/69546.html It works really well for me for general cleaning, I didn't know about it when my deck got stained pink, but it may do the trick.
What I did back then was to dilute regular old chlorine bleach about 1/2 and 1/2 with water and wipe it on with a rag soaked in it. Leave it on for about 3-5 minutes and wash off with soapy water (the soap will help neutralize the bleach). Then rinse REALLY well. You may have to do that 2 or 3 times, but it got almost all of the staining off. I had some very light pink stains left in the stiching, but they dissappeared after about 2 weekends in the sun. I know bleach (especially chlorine bleach) is not reccommended to clean vinyl but I haven't had any hardening or cracking and that was at least 3 years ago...maybe 4.
I put a white sheet between the black cover and the V-Drive vinyl after that incident and did'nt have the problem return.
BTW, I had a new (light grey this time) cover made about 2 years ago and it turned my white rub rail pink when it got hot. I know pink is pimp, but not so much in this case. I tried bleach on that too but pretty much the only things that worked at all on the rubrail were ajax and some sandpaper.