The only thing I can think of (which would validate what @PointC theorized) is that perhaps you're animating SVG elements and you've got transform-related data defined in both CSS and the SVG's "transform" attribute. In that case, the browser has conflicting data about transforms and it just has to pick one. So, for example, if you've got transform: translate(0, 10px)" in CSS, and then GSAP sets the SVG's transform attribute to transform="matrix(1,0,0,1,100,200)", what should happen? GSAP may be setting the values properly, but the browser may be overriding it with the CSS data (which isn't changing).
Updating to the latest version will likely fix that anyway, because at some point we added a workaround for that.
If you still need help, please post a reduced test case with details and we'd be happy to take a peek. Happy tweening!