I have these two problems on two machines as well (both after upgrading
to 16.10). One machine exhibits *just* the two symptoms you describe,
while another also has an odd bug making the numeric/formula entry text
box transparent (see attached).

Interestingly (/frustratingly, confusingly), the menu and transparency
issues are not present when running a guest session on that machine, but
the menu remains an issue in the guest session on the other machine.

** Attachment added: "20161021-2315-transparent-gnome-calculator.png"
   
https://bugs.launchpad.net/ubuntu/+source/gnome-calculator/+bug/1615408/+attachment/4766645/+files/20161021-2315-transparent-gnome-calculator.png

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https://bugs.launchpad.net/bugs/1615408

Title:
  Theming issues with yakkety gnome-calculator in Unity

Status in gnome-calculator package in Ubuntu:
  Confirmed

Bug description:
  There are some UI problems with yakkety's gnome-calculator. I'm
  attaching a screenshot taken with yesterday's daily live Ubuntu image.

  1. The title bar says 'gnome-calculator' but it should say Calculator
  2. The Mode menu has an ugly light-colored border around it instead of being 
integrated into either the title bar (like gnome-calculator 3.18.3 in Ubuntu 
16.04 LTS) or in to Unity's menu bar.

  These issues affect both gnome-calculator 1:3.20.1-0ubuntu1 and
  1:3.21.90-0ubuntu1 but do not affect 1:3.18.3-0ubuntu1 on yakkety.

  I think this was caused by the refresh of
  debian/patches/git_no_headerbars_in_unity.patch in the 3.20 update.

  Screenshots attached.

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