On some boxes I used to config they used to have this issue with ioBanana doing exactly this (very old version of ioBanana BTW, not used in a hella long time so can't comment on current version) but switching to php_pSio seemed to fix things up. I don't know if these boxes were quite that low spec but they were low spec.
With a box that low spec if its a seperate box the best solution would be to install glFTPD. io is the best on windows by far but it can't compare to a linux solution for stability has unfortunately it still suffers from being on MS.
It may take a while to first set-up but its not as hard as you may think.
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