Strange issue with .25mm nozzle

I have a strange issue that I cannot seem to figure out. I am printing plug cover plates for a model railroad with a Robo3D R1 using a E3D V6 hot end. I printed a 1.5mm thick plate with a .4mm nozzle at a .1mm layer thickness. My software is Simplify3d. I have some text in the print that was barely legible with that resolution, so I switched to a .25mm E3D v6 nozzle in the hope that this would help, leaving all the other variables the same. Instead, I got entirely crazy results. I have attached two photos, one showing a side by side of a .4mm nozzle print and a .25mm nozzle print, along with a detail of the .25mm nozzle print. It appears that the layer depth is not .1mm and appears to worsen the higher the layer. I have searched high and low and cannot find anything specific to this situation.

I updated my printer to Marlin 1.1.4 between the prints and am using 8mm rods. I have ensured that the configuration.h file reflects this configuration. I have also ensured that the EEPROM settings have been reset. Not sure what else to do. Any suggestions would be really appreciated.

 

Yes, and layer is set to .1mm. I have verified that my z axis is configured for 8mm rods.

 

I have played around with the speed, extrusion factor, etc. But the bigger problem is z-axis related - if I could solve that one, then I could deal with the print quality issue. It appears that the layer height is being calculated incorrectly and seems to be compounding as the nozzle gets further from the bed. The print should have been the same thickness as the .4mm printed one in the picture. I have created new factory files from scratch to rule out a corrupted file, but the results have been identical as shown.

 

Quick sidebar: Sorry for delayed response. I live in Meyerland in Houston, TX and have been living with Harvey for some time now. No flooding in house, amen, but lost a vehicle. This thread was started while surrounded by water and nowhere to go and had time to fiddle around. That period has ended and I have been distracted with helping many friends clear out their flooded houses and tearing down sheetrock to make them usable as shelter while also worrying what next week will bring wrt challenges to live here in Houston.

I have swapped nozzles. I still cannot even get a decent first layer - I have used UBL and Bilinear leveling configurations to no avail. This has become so frustrating that, paraphrasing WarGames, I have come to the conclusion that 1.1.4 sucks. At least for me. I now have to rollback to 1.0.4, I believe as that worked for me. I am simply baffled as to what could be so horribly wrong that this is my only path to sanity.

Excuse my vitriol, I am just a tad short of patience right now in life.