I've just encountered the very same issues, but without even having any dynamics at all. I've built a set in R18, and each time I've saved (with a bit more within it in each version) the file gets bigger and bigger. And not just a little bit bigger, CRAZY bigger. The current version is 23GB, and took about 6 minutes to save.
I then opening up the same file in R19, which took about 4 minutes to open, saved it as an R19 file, and checked the file size. Now the file is only 2.8MB!
So, not sure what's going on with R18. The only reason I'm still using it is because I've got loads of go-to plugins in my R18, that I haven't migrated over to R19 yet.
Anyway, point is - this issue is still present in R18 clearly.... but has maybe been resolved in R19
I had found a few weeks back that having a Cloner 'active' vs 'deactivating' it before saving (this is in R18) made a huge difference in how long it took to save the file. That doesn't seem to be an issue in R19 (fingers crossed)