The bulk downloader mangles names when there are multiple files with similar names. From one of our users:
There is no issue in uploading, you need to now download what you have uploaded.
I believe the issue is in the creation of the zip file for download.
Here is the test Synapse project to inspect:
Select any two files with the same base name such as dog.jpg and dog.png for inclusion in a download. These files have different names but when they are included in a zip file the names become dog.jpg and dog(1).png.
This is incorrect behavior