Thanks for the many tips - all helped
Correct, is not the radio loop - this appears before and leaves after the crew, with no noticeable effect to frames. Using 'lowered loop mod' made no difference.
As for the file, while using SH3 commander, I did have the 102+ .cfg files in the correct place - the GWX.exe file I downloaded was the one large one (+/-795mb) not the split files - never used the md5 checker, tried to return to where I got the gwx setup, but page has gone (I think was maybe from the GWX pages that I got it originally)
But first I didi was to go back to bare basics - uninstall all, delete all suggested files, then re-install SH3 +1.4b patch, run once, make a back up of this, then install GWX, then 1.03 update.
From here I tested again (nothing enabled in JSGME, did not install commander or sh3 gen).
Still had the same problem with the crew appearing on deck, had a look at the stock sh3 backup i had made, noticed a few differences - wiped the crew files (sh3/data/crew) from GWX, replaced with stock, tested - absolutely no problem

Took it further by putting back all the GWX crew files, then only deleting the few extra TGA's that appear in the GWX folders (compared to the stock tga's - to do with officer bodies, I think) - this helped, but still had a slight slowdown (but not as bad as before) (edit - see tables below)
One thing I have not tried is using stock dat files with gwx TGA or vice versa - not sure if this would crash the game if a dat references a tga that isn't there? (if that what is happening in the dat files.)
For testing I used the same save game, in the middle of the ocean far way from traffic. Inbetween swapping in/out textures/crew files, would exit sh3, do the moving/swapping, then relaunch sh3, load save game and test again.
As time allows will try again with GWX crew, maybe use the JSGE 'no medals' option, see if that gives a help.
Thanks for all help offered here, I think it helped me along the right path..
But a question - if I replace the sh3/data/crew files with stock, is this replacing their abilities, or just their 'makeup' as in clothing, faces, user interface icons etc? ie does this affect gameplay in any other way than appearance/eyecandy?
Also, will I run into troubles later on doing this? eg - while testing I used the same save game, but time taken to test how many sailors/officers was not a lot of game time - might this cause a crash later in the heat of things?
Edit added - FYI frame rates with diff crew file combo's below. Excuse the dots, I do not know how to make tables in posts
....................................GWX + Stock crew......GWX + GWX Crew.......GWX + GWX crew (without extra officer files)
1-3 sailors...........................~62-70....................~59-70....................~59-70
4 sailors(1PO)......................~62-70....................~45-49....................~45-49
4 sailors(1PO) + officer..........~62-70....................~7-8.......................~25-30 (yes, I thought strange also?)
I bow to other peoples knowledge on the interpretaition of above anomalies..