Issues with repetier firmware..Fan and fan2

I have been trying to figure out a couple issues i was having running additional case and digitalWrite or analogWrite with marlin firmware so i decided to try the latest repetier firmware..I am running both repetier host and repetier firmware..Here is the issue i am having.I added the part to the firmware to enable the fan2 so now if i send a m106-m107 or m806-m807 manually from repetier host they work as they should controlling the d6 or d7 pins..But if i send a g code with m106-m107 or m806-m807 they do not work ..So if i run them without any moves or anything else they work as they should but if i run themin the g code they do not turn the pins on or off.I did put the setting for faking the temps to 25 degrees C. this had no effect on them working..I am pretty sure they are not being buffered when there are moves..
Currently i am running a megatronics v2.0 when i was using marlin the m106-m107 worked but the m806-m807 acted real crazy ..They both worked when manually sending the codes.but when it was in the g code it would turn the fan2 off and on like 3 or 4 times real quickly at the start of the code then the next 5 or 6 times the fan2 would be off when it should be on and on when it should be off..Then the next time it should turn off and on it would just stay off....
I then started playing with the g code i deleted all the m106 and m107 codes it still messed up the same for the m806-m807.then i deleted the moves and it seemed to work but it happened so fast you couldnt see the led changing status..Next i decided to add a delay so i could see the change in pin status.. so i added a g04 p500 before and a g04 p1000 after the m806 and m807 .. with this it works so you can see the fan2 kick on for the programmed amount of time and then off for the amount of time ..Next i added the g01 and g00 moves it worked as it should ..Problem is i am using this on a cnc plasma cutter so stopping mid cut for a pause will ruin the cut quality..I ran it from repetier host and from the sd card both did the same thing..SO this tells me it is not a problem with repetier host..It is a firmware issue probably a buffer problem..I have tried it on 5 different computers,6 different usb cables, 6 different controllers(4 ramps 1.4 and 2 megatronics) I tried old versions of marlin and the latest version of marlin and now repetier firmware .. all with no luck ..This tells me it is a firmware issue and has to do with how it is getting buffered....
Any insite of suggestions of what i should try next or where i might find the settings for the buffer would be a big help???It doesnt matter how i write the code or which case i use it does the same thing

N806/M807 is not listed in gcodes section of reprap wiki. So I wonder if you are using a special version where you hacked in the commands. repetier definitely only supports M106/M107. All other fans are bound to special functions like extruder/board cooling.

You have to watch out for buffers. Only with one of the last updates repetier support now in time M106/M107 fan setting. Before it was executed when the command was read independendly of moves in buffer being executed. Could that also be your problem with marlin? It is hard to sync this with buffered moves without interrupting the print flow.

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