Did you clear out the dregs in AppData after the original install and before your install outside of program files? Those may still cause a conflict when the game tries to load.
Since you've installed outside of program files, you can blow away anything and everything related to SHIII in AppData.
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My Father's ship, HMCS Waskesiu (K330),
sank U257 on 02/24/1944
running SHIII-1.4 with GWX2.1 and SHIV-1.5 with TMO/RSRDC/PE3.3 under MS Vista Home Premium 32-bit SP1
ACER AMD Athlon 64x2 4800+, 4GB DDR2 RAM, 400GB SATA HD
Antec TruePower Trio 650watt PSU
BFG GeForce 8800GT/OC 512MB VRAM, Samsung 216BW widescreen (1680x1050) LCD
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