Unresolved Robo3D R1 Plus Print Deformations

I replaced the RAMPS board recently, and it was working OK, but I recognized that my thermistor was going bad (getting 'burned' prints) and the temperature was definitely not staying where it should.

I have ordered new thermistors from Robo3D and they are in the mail...however....while waiting for those to come I decided to just buy another Hexagon from Amazon ( https://www.amazon.com/gp/product/B00W8FL5BS/ref=oh_aui_detailpage_o01_s00?ie=UTF8&psc=1 which is the generally recommended hot end).
I got this yesterday and installed it (used all the parts for the 'hotend' except the fans, I stuck with my originals). It didn't take long, but it doesn't appear to work very well.

I don't have pictures on me, but the best I can describe is that the first 1/2 inch of the print (I'm printing an arrow head for a Hawkeye arrow) comes out deformed and it doesn't print correctly, parts of it aren't printed right at all....The best I can describe it is, it prints in total about half of the cylinder, 2 x 1/4's that are opposite of each other.
HOWEVER, after about the first 1/2 inch, it prints perfectly fine and looks great and I would honestly have zero issues....if it wasn't for that first 1/2 inch.

I'm using a RAFT, my filament is hatchbox PLA, and I've tried using temperatures from 190C up to 215C (this is normally what I used with my original hot end/thermistor). Bed temperature was 50C as per my norm for PLA. I've tried varying lots of other settings, ranging from the extrusion multiplier to print speed. I have not changed my Z offset since changing the hot end, however, I haven't been having issues with it sticking to the bed or jamming/clogging the extruder either.
I've printed this model multiple times with my original hotend, and aside from knowing it was getting too hot (due to the thermistor), it printed just fine.

 

Unfortunately that will have to wait until this evening. I didn't take any of them before heading into work.

Something just doesn't seem right. I don't understand how it could print the first 0.5" of the model poorly, and then print the on 1.5" of the model perfectly. It just doesn't make sense logically. And it's done this for 3 or 4 prints, the exact same way. If it was an issue with being a new hot end, or an issue with the filament, or even an oiling problem (which I did do), I would expect it to happen the same every time throughout the entire print instead of just at the very beginning.

 

I guess my only comment on that regard, is that I'm using a RAFT and it prints the raft just fine. It even appears that the first layer or two are fine.

Either way, when I get home tonight from work I'll take a picture of one of the models I printed.

 

As you can see, the bottom is pretty bad. But it gets better and looks fine (ignoring the very top....).

I'm using matter control on standard settings, nothing funky outside of changing the temp for the PLA.

 

I already have the minimum later time set to 30 seconds, up from 10. It doesn't seem to have any effect in matter control.

 

I guess my big problem is, that if the hot end is indeed the same, why can't I print with this one, but I'm willing to bet if I put the old one on, it would work fine with the new thermistor.

To me, that makes zero sense.

 

Did buy the 12v model.
The part cooling fan didn't have much air flow.
It was a Noctua 12v fan, so I just replaced it with a 5v version of the same fan. Much more air flow. (Yes, I know, 12v on a 5v fan, etc....) The print came out much better now. Not perfect, but close enough. Printed 4 or 5 more of them, and then this morning I started a 20 hour print. We will see how it goes.