The 'single include file' method is the simplest, but it has the disadvantage (as you have seen) that it is single-threading the queries, and will stop processing if it finds a cfg file error (although it will continue if it is just an SNMP error it encounters).
I would suggest dropping toa a 5-min poll cycle unless you really need 1-min else you'll just not have enough time to complete the poll.
If you absolutely must have 1-min then either get a faster machine, or multi-thread. Since I'm a UNIX guy I dont know how you'd go about doing this using Windows services... maybe another Windows person here can help? Also, try reading the help on
http://www.mrtg.org and see if there are more hints there for Windows users.