I too have used Ebay (buyer & seller in the past) along with Paypal.
I look over the invoices once they are emailed to me, then I pay them.
If I do a "Buy it Now", I double check the shipping.
The only time I had a problem was with a new seller that didn't know how to cancel an invoice for an adjusted invoice and it kept showing it was due...I explained to Ebay and sent them the invoices and it was all taken care of.
I've actually had 2 bad fabrics off here (don't bother to look and see as they aren't listed anywhere on my files ...nosy rosy :)) and it was my fault I felt because I didn't double check the fabric when it arrived. I didn't leave feedback because it was my fault for not paying attention.
As they've recommended...you did end up with your fabric (hope you liked it too), got shipping refunded even if it was a small hassle and hopefully you got good feedback from the seller, so I wouldn't leave negative. It sounds like they were willing to work with you granted slowly.
One bad experience isn't indicative of all sellers on Ebay.