when you say POE shield, do you mean shield with POE installed?
I mean the shield you apparently bought with the upload issue notification.
FWIW, I power cycled using external power (not using USB) and it works every single time. So this is not the same issue as the old thread, as I don't remember reading any mention of problem uploading (or I may have missed it).
Below is the old issue statement. This issue would be unacceptable for a PoE board, as it needs to have unattended recovery from a power cycle. I just speculate that the PoE boards may have been modified in some way (possibly like the mod to the old boards) to automatically recover unattened from a power cycle. The mod may also have the consequence of requiring a manual reset during program uploading. Bottom line: old boards don't have issues with traditional uploads, new PoE boards do have issues with traditional uploads.
Problem: Arduino 2009 with wiznet w5100 ethernet shield does not start network operations after power-up.
It works well if the reset button is pressed.