why is this masechta in moed ? Because even though the shekalim are collected at a set time in the year their purpose is for korbonos and therfore its place should be in kodshim.
Good point. We also find that Maseches Chagigah, which deals primarily with the Korbanos and with topics of Taharos, is in Seder Moed. It seems that, as you say, since the topic of Maseches Chagigah is something which is practical at certain time periods (i.e. the festivals), it was placed in Seder Moed. The same is true for Maseches Shekalim; since the announcement for the collection was made at a certain time in the year (before Pesach).
Besides, since the Terumas ha'Lishkah was performed three times a year (in order for it to be publicized), before each of the Shalosh Regalim , it is appropriately placed in Seder Moed among the Masechtos that deal with the Shalosh Regalim.
-Mordecai