Cubes too large and holes too small.

I've struggled to get successful prints of multiple parts that fit together, such as the planetary gear sets you see on thingiverse. I've had similar issues, for example, when I made a filament spindle I had to file pieces down quite a bit to get them to fit together.

To diagnose the issue, I make a test 10mm cube with a companion piece, a 30mm x 30mm x 10mm block with a 10.5mm x 10.5mm hole in it.

When printed, the hole is 10mm x 10mm and the cube is 10.4mm. I have about a .4 - .5 increase of dimension in both sides.

I looked at the instructions on [www.thingiverse.com] . Although I use Slic3r, not Skeinforge, I tried their recommendation of increasing the W/T ratio - from 1.5 to 1.6. It didn't seem to have an effect.

What other settings should I look into? Should I wind down my flow rate?

Lower your extrusion multiplier.

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I had a similar problem and it was hard to nail down. For me it came down to cooling, and maybe this will fix your problem too. I was having with prints fail so I would increase the extrusion multiplier in slic3r. I was printing with a multiplier of 1.8 to get parts to stay together. My prints wouldn't fail, but I wouldn't get holes where I should and parts didn't fit together like I expected. When I printed with the correct values with slic3r, my prints failed after a few layers. I finally added a household fan near my printer to cool the part as it printed and bam! it worked.

I set slic3r back to the multiplier of 1, checked calibration of the printer and double checked the diameter of the filament with a some calipers (checked in multiple spots and averaged the values) and it all just worked. It worked 200% better. I could print small holes, overhangs, and pieces started fitting together. I eventually added two permanent 40x40mm fans to the print head and I've been happy ever since. I almost feel like this should be part of the setup for printers, but its not. Remember when you're starting, its quality not quantity. Its okay if a print takes 4 hours instead of 30 minutes. Its better to have a successful part then a bin of failed prints. Just get it working slowly and thing start bringing in the slack.

I think the secret to a lot of successful printing is cooling, or printing slow enough to allow the plastic to cool on it own. If you look inside commercial printers you'll see that the big secret is a lot of cooling. The printer at work has a ton of 120mm blower fans inside.

Let me know if this helps any. Its just what happened to me, but I don't know what's really happening to your setup.