1. The first step to debugging this and many other problems is to create as simple of an example of the problem as possible. Can you write an example of a simple differential equation which shows this problem?

2. Create Functions. They're the key to good programming for people new to Mathematica. Both Q1, Q2, u1 and u2 are functions that depend on t. So you'd write them as:

   u1[t_] := k1Theta'[t] - (Q2[t] + u2[t])(Theta'[t] + 1)/Phi'[t];

   u2[t_] := k2Phi'[t] - (Q1[t] + u1[t])Phi'[t]/(Theta'[t] + 1);

Start with this. Turn everything that is a function into a function.