Upgrading to a 13s hotend might help, but even with one of those I could never get Ninjaflex to print as well as I needed.
My other recommendation is to print reeaaalllyy slowly; see if that helps.
Unless you need the part to be super flexible, I suggest using Ninja "semiflex." I had much better results using it. However, I've since switched to Sain Smart's TPU
filament for all of my flexible parts. It's half the cost for almost twice as much filament & I can print it at ABS speeds.
Not sure about water absorption, but it couldn't hurt to "cook" the ninjaflex to dehydrate it. I suggest baking a small amount first, just see if it makes a difference.
Finally, I've attached a pic below showing the difference I encountered printing ninja semiflex after switching to a 13s hotend using the same settings. I highly recommend one, it's amazing how much better they print.
PrintrBot Model: 1403 (Simple Metal Assembled) :: DIY Heated Bed, with 305mm Extended X Axis
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