The devs tell me that crew transfer is receiving some attention for 3.30 and so it may be worth waiting for that in beta before testing it again.

This may help

Not sure if I am allowed to quote code here but as its taken me two days to find the cause and a code fix ...

Its a problem with the ai script order.trade.crewexchange in 3.20, it was fine in 3.10

what is does is to loose pods, so if I send 15 marines over that should be five pods but it only sends three leaving 6 marines behind

the problem code is around line 465

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<set_value name="$cap_pods" exact="[$crewtotransfer_active.count, $crewtotransfer_passive.count].max" comment="should provide quite a bit of headroom since more than one person can normally fit in a pod at a time"/>
<do_while value="$poddock_active.isoperational and $poddock_passive.isoperational and (($crewtotransfer_active.count and ($transferredtopods_active.count lt $crewtotransfer_active.count)) or ($crewtotransfer_passive.count and ($transferredtopods_passive.count lt $crewtotransfer_passive.count))) and (@$numpods_active lt $cap_pods) and (@$numpods_passive lt $cap_pods)">
<do_if value="$crewtotransfer_active.count and ($transferredtopods_active.count lt $crewtotransfer_active.count)">

The cause is that the list of nps's to transfer $crewtotransfer_active has npc's removed from it lower down within the do_while loop as the marines are added to boarding pods which reduces $crewtotransfer_active.count

That makes the do_while loop run less times than it should which leaves crew behind on the originating ship. You loose roughly half the pods

if you stash the starting number of npc's to be transferred by adding a couple of variables and alter the do_while and do_if lines to use the starting numbers then the loop runs the correct number of times and I get all my marines transferred

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<set_value name="$cap_pods" exact="[$crewtotransfer_active.count, $crewtotransfer_passive.count].max" comment="should provide quite a bit of headroom since more than one person can normally fit in a pod at a time"/>
<set_value name="$crewtotransfer_active_num" exact="$crewtotransfer_active.count"/>
<set_value name="$crewtotransfer_passive_num" exact="$crewtotransfer_passive.count"/>
<do_while value="$poddock_active.isoperational and $poddock_passive.isoperational and (($crewtotransfer_active.count and ($transferredtopods_active.count lt $crewtotransfer_active_num)) or ($crewtotransfer_passive.count and ($transferredtopods_passive.count lt $crewtotransfer_passive_num))) and (@$numpods_active lt $cap_pods) and (@$numpods_passive lt $cap_pods)">
<do_if value="$crewtotransfer_active.count and ($transferredtopods_active.count lt $crewtotransfer_active_num)">

That fixed my problem

Not sure what the passive transfer bits do but to fix them also change the original line 467 from

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<do_if value="$crewtotransfer_active.count and ($transferredtopods_active.count lt $crewtotransfer_active.count)">

to

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<do_if value="$crewtotransfer_passive.count and ($transferredtopods_passive.count lt $crewtotransfer_passive_num)">

haven't tested this bit