I compared Mathematica's default integral evaluation to what you get by computing the indefinite integral and then plugging in the limits.
(I did this because the latter approach was much faster for some integrals.)
I got two different results:
integral=-Log[-a+b+2 a x+2 a Sqrt[(-1+x) x]]+Log[-a+b-2 b x+2 b Sqrt[(-1+x) x]]
integralDefault=Assuming[a>0&&b>0,Integrate[integral,{x,0,1}]]//Timing
(*I Pi/2*)
integralInDef[x]=Assuming[a>0&&b>0,Integrate[integral,x]]//Timing;
integralDef=Assuming[a>0&&b>0,Limit[integralInDef[x][[2]],x->1]-Limit[integralInDef[x][[2]],x->0]]//Timing
(*-I (a^2-8 a b+b^2) Pi/(4 a b)*)
The first result agrees with the numeric value.
Is this a known bug?