AFAIK, there is an option to activate direct input mode in Japanese IME. Here is the steps to do so (using Windows 7 as sample):
a. Using language bar
Click the drop down button on bottom-right corner of language bar while Japanese IME is being active, click "Properties" to add the menu, then click on it when appears.
![IME Properties Menu](../../I/static/images/38e272f56f371c85c04825cbc28db9aa4736af9d830333c368becf325835c286.png)
When dialog box "Properties for Microsoft IME" appears, go to "Editing" tab, then uncheck "Don't use direct input mode" (as shown in supplementary image).
![IME Properties Editing tab](../../I/static/images/137a8215ce4e7db27b00f598a5ec813e766c1a8df047dbf428c0ad689458ea3b.png)
b. Using "Region & Language Options"
Go to Control Panel => Region & Language => Keyboards & Languages tab => click "Change keyboards" button. The "Text Services & Input Languages" dialog box will appear as shown below:
![enter image description here](../../I/static/images/053618b8f0883e315d6359f677b3f7238470bc9f2e141d58936d36d5ea1a4aed.png)
Select "Japanese - Microsoft IME" & click "Properties" button, then "Properties for Microsoft IME" dialog box will appear and follow same procedure above to uncheck "Don't use direct input mode" option.
NB: Don't forget to apply changes using "Apply" then "OK" button and restart all Office applications which exhibit that small input popup box.
Related issue:
Weirdness with Japanese IME and MS Outlook (also apply for other MS Office programs)