Very large amount of lost/stale shares after replacing bmminer bin file on S9

Hi, I wanted the extra overclocking capabilities of the new May31 s9 firmware, but keep the ssh capabilities of the older firmwares. I unpacked the newest firmware and moved the bmminer file to /usr/bin, the factory bmminer.conf to /config and replaced the pages folder in www in the old firmware using scp.

Bmminer seems to work fine miner side, with the overclocks working properly. The issue is there are now 2.5 times as many stale shares as accepted on average. Pool side I get about 4TH instead of 15.5, and 3.5TH instead of 13.5 in normal mode.

I have an s9 running the newest firmware and it works fine. Its not the network, which is what most google searches lead to.

I ran bmminer through ssh to see the log and there are lots of "lost x shares due to no stratum share response from pool 0", among the accepted share messages.

Has anyone come across this issue? Is there a another file I missed copying over? Or maybe a setting for bmminer in /etc/init.d/bmminer.sh that I should change? I copied the bmminer.sh file from init.d in the new firmware over to the old afterwards as well with no luck.

If it makes any difference, I noticed it takes a few minutes before the lost shares start to show.
Any insight is appreciated.

Thanks!