Unable to reproduce the issue on Win-10 and Ubuntu 14.04 using chrome reported version #60.0.3112.78 and latest canary #62.0.3174.2.

Attached a screen cast for reference.

Following are the steps followed to reproduce the issue.
------------
1. Opened the attached file "open_jar.html"
2. Observed that the open file dialog popup appeared as expected.

Reporter@ - Could you please check this issue on latest canary #62.0.3174.2 by creating a new profile without any apps and extensions and please let us know if the issue still persist or not.

Thanks...!!

Deleted: 751038.mp4 114 KB

	751038.mp4 114 KB View Download

I am testing with Win10 x64 Chrome 60.0.3112.78 and Chrome Canary 62.0.3174.2

Chrome 60 + normal mode: no file dialog
Chrome 60 + normal mode + disable extension: no file dialog
Chrome 60 + incognito mode: no file dialog
Chrome 60 + "chrome.exe --user-data-dir=/new/folder": file dialog with "JAR file (.jar)" appears
Chrome 62 + normal mode: file dialog with "JAR file (.jar)" appears

Note:

- I only have one Chrome extension in Chrome Stable which is Chrome Data Saver
- I have been using Chrome Canary for testing, so Chrome Canary's user data folder is not clean.

I saw the same issue today using version 59.0.3071.86, as was another developer on my team running 58.0.3029.110 (both on Ubuntu). We saw it with an extension of ".zip" instead of ".jar" (and also with combinations of other extensions with .zip, such as ".pdf,.zip"; using ".pdf", ".doc", or ".pdf,.doc" works fine, but if ".zip" is included it stops working). I was able to reproduce it with .jar with additional testing just now my coworker found this bug.
We see this issue when connecting to a server via a public IP (69.x.x.x), but not when using a hostname or an internal IP (in the 192.168.1.x range).

Additional info: If .zip is included with many other extensions, and it is towards the end of the list, the file dialog opens fine.

accept=".pdf,.mif,.ai,.psd,.sdw,.gif_d1,.ans,.asc,.bmp,.cdr,.wpd,.txt,.eps,.xml,.gif,.htm,.jpg,.wk1,.obd,.xls_d1,.xlsx,.msg,.ppt,.pptx,.pub,.rtf,.vsd,.doc,.docx,.wps,.wb1,.pbm,.pgm,.png,.ppm,.ps,.rpt,.tif,.mime,.xyp,.zip,.wp5,.xls,.pps,.fmv,.fm,.jpe,.jpeg,.css,.html,.wks,.wk4,.wk3,.jpeg_d1,.png_d1,.jpg_d1,.fax,.tiff,.sep,.dib,.cur,.ico,.rle,.csv,.xlw,.xlt,.xlc" == file dialog opens

accept=".zip,.pdf,.mif,.ai,.psd,.sdw,.gif_d1,.ans,.asc,.bmp,.cdr,.wpd,.txt,.eps,.xml,.gif,.htm,.jpg,.wk1,.obd,.xls_d1,.xlsx,.msg,.ppt,.pptx,.pub,.rtf,.vsd,.doc,.docx,.wps,.wb1,.pbm,.pgm,.png,.ppm,.ps,.rpt,.tif,.mime,.xyp,.wp5,.xls,.pps,.fmv,.fm,.jpe,.jpeg,.css,.html,.wks,.wk4,.wk3,.jpeg_d1,.png_d1,.jpg_d1,.fax,.tiff,.sep,.dib,.cur,.ico,.rle,.csv,.xlw,.xlt,.xlc" == file dialog does not open (same list, but .zip moved to the front instead of being in the middle)

jtsai@ Thank you for the issue.

Unable to reproduce the issue on Ubuntu 14.04 on latest stable 60.0.3112.90, reported version 60.0.3112.78 and on Mac OS latest canary with the below steps.

1. Opened the given html file on chrome.
2. clicked on 'Choose File' button and a file dialog is opened. No issue is observed.
3. Changed the file extensions in accept value and retried the issue. No issue is observed.

Please find the attached screen cast and confirm if anything is missed here.Request you once try the issue on clean profile and update the thread.

Deleted: open_file.webm 5.6 MB

	open_file.webm 5.6 MB View Download

I'm seeing the same issue, particularly this part:
"We see this issue when connecting to a server via a public IP (69.x.x.x), but not when using a hostname or an internal IP (in the 192.168.1.x range)."

So the difference from the screencast is that in the screencast, the file is served through "file:///". If instead, that file is served off of a public IP, the issue occurs.