Can we tackle second issue?
Why is mach after first touch off goes to machine coord 0,0,0 rater than working cord 0,0,0

Can you explain what it does a little more clearly? maybe a step by step of what you're doing?

After homining etc I lode g-code, then start runing it as per config and m6start it goes to designated tool location I do tool change and touch off in same location.
Press start to continue, than machine goes first to machine coord 0,0,0 than work coord o,0,0 and then to tool path.
Why machine is going to machine coordinates 0,0,0 first? Is there setting in config?

The tool change location on the Settings page is in Machine Coordinates, I think. Are you clicking the Toolchange Pos. button?

It may be in your M6Start.m1s or M6end.m1s macros.

Tool change location is is exactly in M6Start macro

Ok so if the F50 in the inialisation cured your problem it would seem you were meaning that it is the move after the toolchange to the start of the code. I was thinking it was during the first toolpath you were seeing the slow speeds. However if you run in Constant Velocity mode (G64) you will likely see a vast improvement in the speed of the first part of the code due to it being made of many short lines.
 Putting the F50 in the initialisation, although seeming to cure your problem it isnt really as the problem I suspect will be with your M6 End macro in that it is calling a G1 move but not specifying a feedrate. It is also likely that your Machine Coords zero move is also initiated by that macro.
Attach both of your M6 macros and maybe someone will find the problem.
Hood

After speaking on the phone last night, I believe we figured out what he was seeing. The M6 end macro saves the current position and returns there after the tool change.

After he homed his machine, the first time he ran it, it returned to machine 0,0,0 because that's where it was after he had just homed it. On subsequent tool changes, the machine wasn't at machine 0,0,0, so it appeared to behave differently.

THX guys I will test it this weekend when I get home.