ISO Window Contractor AKA - Custom vs. stock

[Matt Vaughn]

Guys, I'm looking for a recommended window contractor in the Laurel, MD area (either Howard or Prince George's County).  I had a budget GC tell me that my 48x48 windows are slightly off of the typical dimensions and will require a custom sized window to replace them.  I find this odd, since I don't know who would build a 3/2 house full of custom sized windows - this is a builder grade home.  

So first, can you throw me a name of anyone reasonable you've worked with?  

and also, does anyone have experience with replacing windows and whether or not that often involves custom sizes or if typical Home Depot style windows work.