Arrghhh first inch of layers is borked, please help

Hi,
I've got a replicator 2 with a glass build plate, aluminium arm supports (which are attached to the plastic arms - not full replacements), fully enclosed surround. upgraded hot end so I can print in flexible, abs, etc
My prints have been fine up till now then all of a sudden the first inch or so of layers are all wobbly and messed up. I've tried feeling the glass plate as i jog the z axis up and around that area and I can't feel any bumps or anything. Any idea what could be doing it or how best to remedy it?
http://imgur.com/a/PbdnP
here's a few pics of the printer in case you see anything that might be causing it
http://imgur.com/a/NK3b0
I'm using Makerware latest version, and their firmware. via USB. I've just thought I could try printing just via SD card but wouldn't have thought network congestion or something could cause the issue could it?

Thanks

Mark