We have no experience of this problem, so it may well be specific to your computer or software, in which case our ablity to help is limited.
Things to try:
The latest version of the drivers are always on the Eventide Web site, so try (first) un-installing your current setup and then re-installing the new ones. There will be a further driver release later this year (date not currently available).
Once this is done, thoroughly exercise the firewire link using only things that come with Windows.
If this works OK, try your sequencer. If the problems now appear, the sequencer software may be at fault.
H8000FW Windows drivers come in both ASIO and WDM versions – if possible try the one you are not currently using to see if it makes any difference.
If you are running 96K, see if the problem also appears at 48K.
Regarding your clocking issues, you may want to look at previous posts on this subject. Esssentially, you need to select one part of your system as the "clock master" and make sure that everything else is solidly locked to it. Wordclock is usually best.
Firewire clock should only be used as a last resort, as it may not be very stable.
You can only use internal on the H8000 if you have declared the H8000 to be the clock master, in which case everything else must be locked to it, including sound cards, which are not always lockable in this way.
Clocking issues really fall into the subject of installation design – if the above is not clear to you, you may need assistance beyond that which we can provide.