The team rankings are a human poll. they don't go to computer polls until after the NTI.
The singles and doubles rankings are based on the players' best # of wins. The # they count increases during the season. So, in the first poll they might take into account a player's best 5 wins, but several months later they're being ranked on their best 10 wins.
So, your ranking isn't just based on whether or not you're winning, it's based more on who you beat. So, Clayton and Thacher have dropped because they didn't beat enough people with a decent ranking. Virginia's #6 player, Justin Shane, has not lost since the January 4th rankings, but he is unranked this go around because his list of victories isn't good enough to get him in, especially with all the #1 and #2 spot players that did poorly in the fall starting to get some dual match victories over higher ranked players.
Early on, one or two big wins can get you into the Top 25, but to sustain that ranking, you have to keep racking up victories over top talent. It's pretty hard for talented players at the #3 spot or lower to maintain their fall rankings. Even if you're on a top team that plays a difficult schedule, you just aren't going to get the matches against top talent that players in the #1 and #2 spots get.