I booked reward flights on the Aeroplan website for the following:
BUF>EWR>PHX and returning SFO>EWR>BUF. All flights on United
I intentionally chose the departing itinerary because it included a 9hr 45min stopover in EWR, which we planned to use for some time in Manhattan.

When I looked at my booking receipt from United, it mentions a $25/bag fee for BUF>EWR AND another $25 for EWR>PHX, yet only one fee for the return trip.

I spoke to someone at United who told me not to worry, and my bags would get checked through all the way to PHX, but, I would in fact have to pay $50/bag since the itinerary involved a stop of more than 4hrs. Then, she double-checked with someone, and told me that I would in fact have to claim my bags in EWR, and re-check-in - which essentially kills the whole NYC plan.
I don't have total confidence in United customer service right now, but it seems very strange that I would have to claim bags and check in again, seeing how it's booked. This can't be right, can it? Anyone with similar experience?

Thanks.