I looked up some of the relevant passages from the Church Handbook of Instructions. I will first quote the handbook (pg. 134), and then give some of my own comments.

"The First Presidency has written: "The simplest statement we know of is the statement of the Lord himself, namely that the members of the Church should pay 'one tenth of all their interest annually,' which is understood to mean income. No one is justified in making any other statement than this.""

[skip a bit]

"The bishop holds tithing settlement near the end of each year. In urgent cases when the bishop is absent, the stake president may authorize one of the bishop's counselors to conduct tithing settlement.

"All members should attend tithing settlement to make sure their contribution records are correct and to declare to the bishop their status as tithe payers. All members of a family should attend tithing settlement. In addition to reviewing the members' tithing records, during tithing settlement the bishop can discuss the principle of tithing with them, encourage them to give a generous fast offering, and discuss other relevant matters."

My comments-

I think the comment "No one is justified..." says pretty clearly that only the individual may determine what constitutes a tithe for their particular circumstance. In other words, in my opinion people (bishops included) who tell a member whether he should pay on gross vs. net earnings, have overstepped their bounds. Of course, counsel may be given (I have heard of one case where a member routinely deducted from his tithing checks $10 an hour for church work he performed-- that guy should be counseled!), but I also thought it was interesting that nowhere does it say that the bishop should judge whether or not the individual has paid a full tithe. Rather, the individual declares his own status.