Early last year I upgraded my scanner to the Epson 3200 photo. For the most part I was pleased with the results. Last week I encountered some problems and had to reinstall the scanning software. I am just wondering if there are any of the default settings that come installed that might need to be changed, or if there are any other recommendations, suggestions or tips that will give me the best scans available,

It's a very subjective thing, but I generally keep all auto functions on my 3200 off (I believe the default is ON). Not all of them are obvious, you may need to open some advanced options.

I do recommend calibrating your scanner (mine came with the Monaco package, which worked well after I figured out that I had to rotate the target scan before starting the calibration). If you didn't buy the pro version you can get several other calibration packages.