Yes—at macro distances, several things make sharp handheld shots much harder, even with IS. First, depth of field becomes extremely shallow, especially at wider apertures, so even tiny movements can throw focus off. That makes focus-and-recompose a poor technique for macro: moving the camera even a few millimeters can shift the focal plane away from your subject.

Second, camera shake is effectively magnified at high reproduction ratios. IS helps, but its benefit is reduced near 1:1, so 1/100s may still be too slow to avoid blur. Also, if the subject moves, IS cannot freeze that.

Common macro practices are to take multiple frames, use manual focus, add more light or flash to freeze motion, and sometimes use a monopod or something to brace against for extra stability without losing mobility.

In short: the softness is likely due to a combination of very shallow depth of field, movement from focus-and-recompose, and reduced IS effectiveness at macro magnifications.