They had to calculate jump fast to join the fleet and the only way was to break the taboo - connecting the computers.

Cylons seized the opportunity and despite of the software firewall they managed to periodically disturb this network. In the end all computers were disconnected. IIRC Gaeta later had to wipe drives and install operating systems again, from these fancy octagonal "cds".

Found the clip: https://www.youtube.com/watch?v=6CkDyc1TLrQ