Digital BW, The Print

From reading this, it sounds like you are doing things correctly. 
Obviously, you are bound by the way that Epson designed the ColorBase 
software, so unless you are having measurement errors there, it seems 
you are doing things correctly. So I can't really suggest why that 
calibration is worng. And of course when the calibration is loaded, 
if it is wrong, that might wreck the profile you make for the printer.

The only thing I can think of, besides a hardware defect with the 
Pulse, is that maybe the OBA in Archival Matte is causing a problem. 
Are you using the regular Pulse spectro, or the Pulse UV cut spectro.

If you have the spot reading attachment, you could measure the 
ColorBase patches to some sort of a text file, and then look at the 
measurements and see if any stick out as being either bad 
measurements, or a print problem. After that you may need to find 
someone with an i1 or even another Pulse to use to check your spectro.

To get measurements into a text file, you can use the free utility 
from Xrite called ColorPort, I don't have the exact link at the 
moment, but a search of the Xrite USA web site always seems to find 
it for me. You'll have to make a custom target that has the correct 
number of patches, and once you save that target, you could probably 
ignore the resulting TIFF image. Then you can measure your ColoBase 
targets, and save the result as either Lab to a text file, or I think 
it will offer desitometric values to a text file too. If you want 
spectral values, along with Lab, then save as a CGATS formatted text 
file. If you can tell me exactly how many patches of each color there 
are, and how many per row (including gray patches to fill out the 
row), and how many rows of each color, I might be able to make the 
Colorport target to get you going faster. A picture or scan of the 
printed target would be helpful too.

Also, where are you located, maybe someone will be nearby, or at 
least easy to send the print too, that has a different spectro. 
ColorBase says it supports remote measurement, as long as the correct 
driver is loaded. And the new drivers should load with out having the 
proper printer connected.