If you've eliminated all other causes, and the shoes otherwise fit well, it'll be the pronation of your foot fighting (therefore rubbing) against the support of the shoe. This is probably something you are unlikely to be able to avoid in a support/motion control shoe, as by design they are in some way trying to force your foot in a different position.
Some people can manage running in neutral shoes with an orthotic (off the shelf, or custom), but some of us find that the blisters are just as bad. It might be wise to at least take the advice of a podiatrist or specialist physio if this is the route you want to try. Orthotics can be a minefield, and a good pod or physio should be able to tweak orthotics to minimise if not elimiate the blistering.
As Debra says, you could try running in neutral shoes without anything else...if you build up slowly, and depending on your gait and footstrike you might find that you suffer no further issues with blisters or otherwise. Just be aware of the differences between aching from increasing training, and niggles which are the start of an injury (should always be the case anyway). Depending on your biomechanics and what exactly your feet do, a trip to a physio for some advice on strengthening exercises to prevent these kind of injuries might be something you would want to consider.
In short, it's really a case of doing what you are already doing and trying different things to see if that works for you.
One thing that I've found in preventing blisters is keeping my feet really dry helps. I tend to start forming blisters once my feet start to get hot and damp. I use an antiperspirant on my feet before taping or using a silicone based lubricant with the thinnest, wickiest socks possible (I find vaseline and body glide don't really hang around long enough to do the job, whereas the silicone based lubricants seem to last better - but are more expensive). It hasn't eliminated my blistering, but has helped.
Edited: 24/09/2012 at 19:19
