Hmm...this is getting bizarre. I think I may be dealing with a dimensional control issue as heat soaks into the printer mechanics.

Here's what I get if I print a single part in the middle of the bed (10x magnified):

2015-06-30 07.10.14.jpg2015-06-30 07.14.30.jpg

And here's what I get if I print a whole bed of 21 identical parts:

2015-06-30 07.08.06.jpg2015-06-30 07.15.11.jpg

The only difference between these parts is that the first one was printed by itself (about 12 minutes) and the second one was printed as a part of a batch that took 3.5 hours. I used Slic3r 1.2.9 stable with the same settings for both (3 solid layers, 2 perimeters, 40% infill).

My working theory is that as the print continues, heat is soaking into some part of the printer and closing up the Z height of the nozzle (warping the bed, expanding the hot end, something else?). The part should be exactly 7mm high. When I print one by itself, it comes out clean with a measured height of 7.11mm. When I print the entire plate, the bottom layers look squished and the overall height is only 6.55mm. The upper layers of the part look fine and the printer LCD says it's at 7.00mm after the print.

So I'm hypothesizing that my Z distance is closing over the first 30 minutes to an hour of the print, squishing the first few layers. The single part finishes printing before the effect is noticeable.

Has anyone else seen anything like this?