We're using the Server-side Form Post method described at https://community.marketo.com/MarketoResource?id=kA650000000GsXXCA0 but noticing that Marketo will only accept about 3 at a time without missing anything.
Is there a throttle/limit that we should be under for this?
I do not believe that there is any throttling in place. You may want to log a support case for this, including some timestamps of POSTs and example POSTs if you do.