Hmm, could this be the bug mentioned in script_patches.cpp:
// Starting in PQ2 1.002.011, the introduction runs too fast. The speed test was
// changed to run before the introduction but this introduced a bug where the
// game speed wasn't restored from the temporary fast speed used for the test.
//
// We fix this by restoring the game speed to the correct default value. Since
// we're patching the speed test anyway, we also disable it so that it returns
// the maximum value without delaying game startup.
//
// Applies to: All versions, although the speed bug is in 1.002.011 and later
// Responsible method: rm99:doit
// Fixes bug: #5496