Were your project sample rates different?
Latency is a factor of the buffer "block" size, in samples, multiplied by number of "blocks" (buffers). That number of samples, divided by the sample rate, is your latency. So if you are using 48 KHz for one project that has 12ms/12ms latency, and don't change your audio buffer settings when you're working in a 96 KHz project, that 96 KHz project's latency will be 6ms/6ms.
This doesn't mean increasing sample rate is a "magic bullet" to achive lower latency, in itself. It will require more CPU, so it might cause dropouts/glitches if you push things too far trying to get the lowest possible latency at the highest sample rate. You can try it though since there's no harm. If your audio driver won't allow a low latency setting at 48 KHz (you can't reduce your buffer/block size) but it does allow a low latency setting at 96 KHz...as long as it works, run with it.