I agree with @David. I have a Synology 920+ that is the same way at times. Although, as you say in this instance that the rest of the system responds adequately, I think the issue here is Nautilus itself.
Each program decides how it will access a piece of data. If nautilus uses a different system call, or a call from a different library, then the side effects will likely be different as well. Perhaps the method getting called under the hood is not responding well with rsync, or it could be a different reaction altogether.
Regardless, the result is the same. I do not see it being something that you can control without switching your file mgmt. gui.
One way to find out without any loss is to download another similar app, and run it alongside nautilus. Switch back and forth for a week or so, and any difference should be apparent.
Another option, if you know the destination path beforehand, is to navigate via terminal to the directory that you need and open from there. This can be done with a single command:
cd <PATH> && nautilus
where is to be replaced with the actual path. If the destination is a file, the command is:
cd "<PARENT-PATH>" && nautilus "./<FILENAME>"
with the same replacement for . Using double quotes will provide a layer of safety from things such as spaces in file pathnames, but will still let bash expand symbols like ./, ~, and *.
