Sounds like you've played SH3 enough to know how things work.
Only thing I can think of; there's not enough crew in the diesel compartment to start/run the engines.
Or, sometimes Sh3 has a type of delay, after issuing a throttle-command. Might try upping time-compression, then hit the throttle. Or maybe the sub is damaged(?).
I've never heard of this type of problem before.
Oh other thing, if you're in a sub-pen, bigger subs get 'stuck' in them, unless the proper mod(s) is applied. A fix for that is here:
----snip-------
STAVINSKY'S SUB-PEN MOD
SUB-PEN MOD: FIX SO IX AND BIGGER SUBS DON'T GET STUCK IN PENS, AT:
http://membres.lycos.fr/stavinskyely...mpaign_LND.mis
-------snip----
If you DL this, just copy/paste the text displayed with your browser, save as "Campaign_LND.mis" and copy-over your old campaign_LND.mis file.