I don't know where you would have read that it's not a good idea to leave ipv6 on? It could be a security recommendation for those not familiar with it, but I can't see why it would be an issue as long as your firewall rules were appropriately set for users? I suppose it might load the CPU more than necessary if you aren't using it? In fact, I actually had to enable it for a customer recently who uses IPv6 as the primary and preferred protocol (human genetic stuff).
The only reason in your case I can think that it started to work after enabling it, would be that the transmitting client was actually using IPv6? I've noticed some clients these days will use IPv6 in preference to IPv4 if they get issued and IPv6 address or have one configured. Is that possible in your case? Check the client settings, or sniff its transmit packets to check?