Ok so after running a new logic analysis tool I did a whole bunch of before and afters.
IDE 1.5 with direct register manipulation for 8E1
IDE 1.5 with Serial.begin(9600, SERIAL_8N1)
IDE 1.5 with Serial.begin(9600, SERIAL_8E1)
And it all tested good... accept I noticed one little difference between IDE 023 and IDE 1.5
I was using the serial.print command which in 023 output true bytes. In IDE 1.5 it outputs ASCII
Changed to serial.write and it fixed the issue
Only probably I have now is that the performance of the SDCard library i'm using has gone from about 8-7 times a second down to 3-4 times a second which is far too slow for my needs. Even after some tweaks, its just very slow.
Ill try mucking around with formatting of the cards.
Thanks all that pitched in to help solve this.