Hi,
I'm glad to hear that things seem to be working better. Unfortunately the change from FactorySQL to Ignition is a major technological shift, but on the whole we haven't come across anything that would really prevent the transition. The performance of the SQL Bridge is equal to or better than FactorySQL in almost every way. The tricky part, unfortunately, is always with OPC... the technology (COM) and the nuances of each particular OPC Server. We've continued to test the OPC-COM module at the OPC Interop events as we did FactorySQL, but the down side is that generally only the best opc servers go the event to begin with 
This is hard to say, because it could simply be something that the OPC server is going to send on startup no matter what. That is, the behavior is 100% defined by the particular opc server, and I would bet that all of these messages are just from one of them, while your other servers don't do it. It could simply be the server's way of sending a "null" value, which in general isn't really possible in OPC. So, if everything is good after startup, I wouldn't worry much.
what is the recommendation about Java versions?I would recommend choosing Java 6 when possible. We now feel confident that Ignition works perfectly well with Java 7, however, we've found a number of changes in Java 7 that have affected performance a bit. In particular, launching clients/the designer can take considerably longer. We haven't seen anything that really affects the gateway, but overall, Java 6 has a longer and better track record for us.
Regards,