I think people will need more information to try and work out what is happening and potentially why. The following details may provide a starting point for further investigation.
1. What version and build of Moneydance are you using. The first 6 or so lines from your Moneydance console window will show this.
2. How long have you been syncing with the iPhone
3. What connection type are you using for the original desktop
4. Is there a pattern of any sort that links the missing transactions.
In some of the questions I am trying to see if there might be a reason for some transaction to not have been copied to dropbox. As you are having problems with Investment transactions your iPhone would likely be unaffected as the mobile app does not handle investments.