For that reason you should basically never enable ethernet flow control except for on a Fibre Channel over Ethernet SAN, and even then they had to invent Priority-based Flow Control to make it sane. If this is a managed switch then you should be able to disable it.
(I used to also work at an ethernet switch vendor.)
Yep, this is much more likely than that it's accidentally forwarding the pause frames. The magic phrase to google here is "head of line blocking": https://en.wikipedia.org/wiki/Ethernet_flow_control#Issues
For that reason you should basically never enable ethernet flow control except for on a Fibre Channel over Ethernet SAN, and even then they had to invent Priority-based Flow Control to make it sane. If this is a managed switch then you should be able to disable it.
(I used to also work at an ethernet switch vendor.)