Thanks for reporting this.
I can reproduce the problem: if I update using the built-in update mechanism (which uses a .zip file), the position is lost. However, if I "update manually" by installing using a downloaded .dmg or a downloaded .zip, the position is preserved -- even though the binaries that end up in /Applications are bit-for-bit identical (and are signed).
But it may take a while to fix. It appears to be a problem with Sparkle Updater (the software we use for updates). It's a lot of work to incorporate our changes into a new version of Sparkle (assuming that a new version fixes the problem) because we modify it quite a bit to increase security (by requiring signed appcasts, for example).