Cutting Outside cuts Larger, Inside Smaller

I've been lurking here for quite a while and finally got my first machine together and I'm looking for a little guidance, I can't help but think this is something that's been covered somewhere but I'm having trouble finding an answer. I have a screw driven Workbee CNC with Stepper Online Drivers and motors ran by LinuxCNC 2.7 on an older PC and doing design and CAM on Fusion360 with a post processor that incorporates G64 from a user here(Spangled). I Have been cutting small test pieces of 3/4 plywood to work out the bugs and have come up with one I can't figure out. My test piece is a 2" x 4" block with a 1' square and 1" circle cut out. The 2" side is .045 over the 4" side is .030" over and the holes are both .045 under. I have also cut a some .750 holes that come out at .705. All of this is done with a .125" end mill that measures .125 and runs true. Tool compensation is taken care of by Fusion 360 and G40 is active and not changed by the program. Just to be safe the tool is also setup as 0 diameter in LinuxCNC. I have verified the steps per inch to be within a few thousandths on a 48" run, way better than I expect in practice. I don't seem to have any problems with lost steps, that was a whole different learning experience. I am all out of Ideas and any help, even what to search for, would be greatly appreciated.

Hi the trick is to use a ZERO Cut Path
and let the Controlle do it by offseting the PATH G41/G42

you can use Every Diameter from the Tooltable with Every Tool and Offset D

So load tool 2 T2 this gives you the H2 for length and D2 for diameter

BUT you can do G41 D4 to set a other offset to the Path

Thanks for the suggestions. Unfortunately I am not well versed in editing g-code so turning off all compensation and manually editing in G41/G42 is well beyond me. I did somewhat take your suggestion and changed Fusion360 to Machine Compensation where it will insert the G41/G42 codes where necessary and I updated my tool library to the actual bit size. This resulted in the 2' and 4" sides being .035 and .075 under respectively. Interestingly enough the square and round holes are now pretty close to dead on but the quality of cut is horrible, it almost looks like the holding tabs caused some type of problem because the cuts move way off track in their vicinity. There just doesn't appear to be any pattern to whats going on. Tomorrow I believe I will try the machine compensation again after I double check all the settings in Fusion360, maybe I have messed with it enough that I changed something I forgot about.

I designed a new test piece, similar to the last, to make sure I hadn't done something I didn't realize. I believe that machine flex is causing some of my issues so I ran off 2 of these at slower and much slower speeds both with an extra finishing pass. I changed compensation back to in Fusion360 and cut one with the actual cutter diameter set in the tool library and the other with it set to zero, this as expected made no difference. The pieces are within a couple thousandths of identical, pretty good I feel for scrap plywood, but the dimensions are still off. The outside dimensions are .065 over, half the diameter of the bit which doesn't make any sense to me. A round hole was cut using an adaptive clearing strategy and it is .065 under. A square hole was cut with a profile strategy and it is only .032 under. All of the off-ages are half or quarter bit diameter which I can't decide if is meaningful or coincidental?

Siily question. Do you mix by any means somwhere radius and diameter?

Actually I never thought about that, unfortunately I just checked and I have it correct.

I am starting to think it's something mechanical. I just cut a piece that has 8 1.125" holes. 6 of them came out exactly 1.100" and the other 2 1.090" but all were within a couple .001 of perfectly round. The spacing of the holes was somewhat erratic but within .010". I so no correlation to an axis with the off-age. Keep in mind I'm measuring MDF with a caliper so my measurements probably are +/- .005 if I had to guess.

Does anybody have an idiot proof way to diagnose this type of error? I have done just about everything I can think of. I can't feel any backlash and my steps per inch are dead on. I am cutting super slow, 15-30ipm and my acceleration is turned way down to 2.5in/s.

I kinda sorta had similar issues until I took actual measurements of the tools. Just because I have a 6mm bit doesn't mean it's 6mm. It actually measured at 5.7mm. This accounted for holes too small and bosses too big.