@Steve *********
ok, as your 90 day report was due next week, you are actually on an "Extension of Stay" as Tod Daniels suggested. Once you were granted that twelve months Extension of Stay, it cancelled out the original visa. As I mentioned in my previous comment, terminology is important so that others know exactly what you mean when you are here asking for help. It also avoids people new to these things from getting confused.
Yes, as you said, since you left Thailand, with a re-entry permit, your 90 day report will be due 90 days from when you arrive back in the country. Count the date you arrive back as day 1 in your 90 days, whether you arrive back in Thailand on the first flight arriving in the morning, or last arriving flight of the day. The 90 day report is only required if you're going to spend at least that many days consecutively in the country. It seems that most Provinces require the first 90 day report after returning from another country, to be done in person at the local provincial Immigration Office, then subsequent reports can be done online if it's more convenient. When you're back in Thailand, it is best to go to the Immigration Office in the Province where you live and ask them for their specific requirements, as each office varies a little.
@Tod ********
will, I'm sure correct or add to what I've said and you can guarantee he knows his stuff.