Sorry, I must have overlooked your first post. Thanks for your report!
The task bar button visibility was fixed in 5.6.0 beta already.
I have added the progress bar bug to the tracker now (fixed already):
https://winscp.net/tracker/1240

Can you send me an email, so I can send you back a dev version of WinSCP for testing? Please include link back to this topic in your email. Also note in this topic that you have sent the email. Thanks.

Would be nice to know if this is a known issue or reproducable. :)

This bug has been introduced a while ago, maybe about one to two years ago, I think. It still happens in WinSCP 5.5.5.

I am using uploading files using the "Send To" context menu shortcut entry in Windows Explorer which can be created by the WinSCP installer.
A while ago, the upload progress window was visible in the task bar, so you could easily read its progress and switch to the window if necessary. This is no longer the case, so it's hard to track progress, and when using the "minimize" button in this window, it becomes completely invisible.
Sometimes, the dialog shortly shows up in the task bare when reaching 100%.

In case it's relevant, I'm using Win7 x64 with the "classic" (Win2k) theme, not Aero.