Huh, interesting. Apparently this happens in USB Loaders when used on the Wii and Wii U, even they have issues with subtitles getting out of sync for some odd reason. Maybe the game itself has some funky undocumented behaviors?
Custom Desktop -
CPU: Intel Core i5 3570 3.4 GHz to 3.8 GHz (Turbo Boost)
GPU: MSI nVidia GTX 660 2 GB GDDR5
RAM: 8192MB DDR3 SDRAM PC2 10600 1333MHz
OS: Windows 7 Professional 64-bit
HDD: 1 TB Western Digital 7200RPM HDD
CPU: Intel Core i5 3570 3.4 GHz to 3.8 GHz (Turbo Boost)
GPU: MSI nVidia GTX 660 2 GB GDDR5
RAM: 8192MB DDR3 SDRAM PC2 10600 1333MHz
OS: Windows 7 Professional 64-bit
HDD: 1 TB Western Digital 7200RPM HDD