The install for Syndicate has been updated a lot over the past year or two. Make sure you're using the latest version (of WHDLoad as well). Other timing troubles can be traced back to the nature of the game's slave - it's just the way they operate when hacked to run from HD.
Screens that display for just the right amount of time on floppy are usually to mask a loading operation. Since a hard drive or RAM (if PRELOADed) is infinitely faster, those screens just flash by. This happens in the Superfrog Intro as well. ButtonWaits or BlitWaits might help here. Check the WHDLoad docs for details on those options.
I usually like the NOAUTOVEC tooltype as well.
If the timing seems grievously wrong, report it as a bug to the author of the install.
