I just copied and pasted the results directly from Mathematica. And yes, the arguments within ArcTan change after the same expression is run more than once in the same Kernel. That is what doesn't make any sense.
I ran your script and I still get False for comparison.
In[1]:= i1 =
Integrate[(m0 v^3)/(c^2 (1 - v^2/c^2)^(3/2)) + (m0 v)/
Sqrt[1 -
v^2/c^2] + (m0 v^3)/(c0^2 Sqrt[
1 - v^2/c^2] (-1 + v^2/c0^2)^(3/2)) - (m0 v^3)/(c^2 (1 -
v^2/c^2)^(3/2) Sqrt[-1 + v^2/c0^2]) - (m0 v)/(Sqrt[
1 - v^2/c^2] Sqrt[-1 + v^2/c0^2]), v]
i2 = Integrate[(m0 v^3)/(c^2 (1 - v^2/c^2)^(3/2)) + (m0 v)/
Sqrt[1 -
v^2/c^2] + (m0 v^3)/(c0^2 Sqrt[
1 - v^2/c^2] (-1 + v^2/c0^2)^(3/2)) - (m0 v^3)/(c^2 (1 -
v^2/c^2)^(3/2) Sqrt[-1 + v^2/c0^2]) - (m0 v)/(Sqrt[
1 - v^2/c^2] Sqrt[-1 + v^2/c0^2]), v]
i1 === i2
Out[1]= (m0 (-2 v^2 + 2 c^2 Sqrt[-1 + v^2/c0^2] -
Sqrt[c^2 - v^2] Sqrt[-c0^2 + v^2]
ArcTan[(c^2 + c0^2 - 2 v^2)/(
2 Sqrt[c^2 - v^2] Sqrt[-c0^2 + v^2])]))/(2 Sqrt[
1 - v^2/c^2] Sqrt[-1 + v^2/c0^2])
Out[2]= (m0 (-v^2 + c^2 Sqrt[-1 + v^2/c0^2] +
Sqrt[c^2 - v^2] Sqrt[-c0^2 + v^2]
ArcTan[Sqrt[-c0^2 + v^2]/Sqrt[c^2 - v^2]]))/(Sqrt[
1 - v^2/c^2] Sqrt[-1 + v^2/c0^2])
Out[3]= False