+1 on finding a new LBS. Skinny tires are fine for commuting, but running fatter tires with less pressure equals a more comfortable ride. With skinny tires and potholes you really need to be careful about were you are riding because you could get a pinch flat or worse (rim damage). In my last year of commuting I had one flat that was actually a torn sidewall. My coworker riding 3 miles each way (compared to my 10 miles each way) often had multiple flats in a week. He even had two in the same day. He is riding a fixed gear bike with 23 and I am ridding a touring bike with 32s. My commuting duties this year will get split between a vintage touring bike, new touring bike, and two cross bikes depending on my mood and the weather.
My biggest reason for wider tires is my commute has two miles of dirt roads before I hit pavement. I wouldn't want to ride 23mm tires everyday for that. The smallest I would go is 28 and I find I prefer 30-35mm tires for that (either touring/road tires or cross tires).
Oh, one more thing for commuting get a rack and panniers. A backpack/messenger bag is fine for short trips and I was commuting with one for a few months before I got a rack and panniers. Since I got them I always commute with them, no more sweaty back and I feel much more comfortable on the ride to/from work.