Hi guys,
Sorry that you seem to have had a bad experience with Focusrite Technical Support, obviously this is something we would like to resolve moving forward. If possible, please could you let me know your email case numbers so that I can investigate further, I would like to check these so we can ensure that all customers are sent information that is both helpful, informative and not irrelevant to your case. You can PM this information if you would prefer.
With regards to Pro Tools, we do see some fairly consistent niggling issues with it on Windows, such as the above mentioned issue with deselecting device within Windows I/O & only selecting it with PT playback engine. It also seems to be extremely sensitive with regards to how sample rates are set between Windows, the session & Mix Control.
Its good to know that you're up and working again, obviously a system wipe/restart is not ideal, but this may have straightened out a deep system/registry issue that may have been causing issues with your Firewire card, causing dropouts.
As well as the above, dropouts are are often caused by DPC latency, an interrupt request by another driver/hardware combo that is preventing your PC from streaming audio in real time. To check if this is indeed the issue, you could download the DPC latency checker from this website, you can monitor the graphs to check for spikes that could be causing audio issues :
http://www.thesycon.de/deu/latency_check.shtml (Win 7)
http://www.resplendence.com/latencymon (Win 8)
If this is mainly happening when recording, as opposed to playback, then please run the software while running your DAW at the same time.
Hope the above helps.
Simon // Focusrite Technical Support