In 6.3.beta4 (so with #13973), I get:

sage: eq = sin(x) / x
sage: integrate(eq, x, -1e-6, 1e-6)
-I*Ei(1/1000000*I) + I*Ei(-1/1000000*I)
sage: _.n()
3.14159465358979
sage: integrate(eq, x, -1e-12, 1e-12)
-I*Ei(1/1000000000000*I) + I*Ei(-1/1000000000000*I)
sage: _.n()
3.14159265359179

Something bad happens with the integration computation when crossing over 0 as we have:

sage: integrate(eq, x, 1e-12, 1e-6)
-1/2*I*Ei(1/1000000*I) + 1/2*I*Ei(1/1000000000000*I) - 1/2*I*Ei(-1/1000000000000*I) + 1/2*I*Ei(-1/1000000*I)
sage: _.n()
9.99999000050877e-7