I have logged on every day since I started playing,, but this morning when I logged on, the bonus for doing so said 'Day 1'......does any one know why, or have I lost all the sequence of the previous 90 days. 

dont worry your paragon has reset. check the paragon run time to validate these. if you notice some irregularities with paragon run time contact support. Paragon run time shouldn't reset after 90 days but continue to 91. but the paragon dailly reward goes back to day 1 after 90 days

I have logged on every day since I started playing,, but this morning when I logged on, the bonus for doing so said 'Day 1'......does any one know why, or have I lost all the sequence of the previous 90 days. 

The daily log on thing doesn't reset anymore for you missing a day.  So you must have gotten the 90 day reward and now you're back on day 1.