Custom keyboard layout: Command+V doesn't paste in Safari and Mail
I'm not surprised you may be experiencing this issue with Apple Software. Basically the Command-. keyboard shortcut has been used by Mac OS for decades as a universal "halt operations" keyboard shortcut. 

In a sense it works in a similar way to the ESC key. So I am thinking this is why you are experiencing problems with this keyboard shortcut. It used to be that software developers had to respect this Command-. keyboard shortcut for any software they developed for the Mac platform, but this is no longer the case, hence why your keyboard shortcut may be working with some software but not others. You may want to read the Keyboard Shortcuts page in the macOS Human Interface Guidelines.

Extra Info

Apple first introduced the Command key in 1980 with the Apple III computer.

The purpose of the Command key was to allow users to enter keyboard commands in applications and within the operating system. The Macintosh Human Interface Guidelines have always recommended that developers use the Command key (and not the Control or Option keys) for this purpose. 

A small set of keyboard commands (such as cut and paste, open and save) are standard across all applications. If an application needs more shortcuts than can be obtained with the twenty-six letters of the English alphabet, double modifiers such as Command+Option are used.

The Macintosh keyboard's other unusual modifier key, the Option key, serves as a modifier both for entering keyboard shortcuts and for typing text — it is used to enter foreign characters, typographical symbols, and other special characters.

As mentioned previously, the Command-. shortcut was once a universal recommended shortcut, but this is no longer reserved by macOS. In fact, Table 67-3 of the macOS Human Interface Guidelines now only lists one keyboard shortcut with a period (.) in it. This is the Control-Option-Command-. keyboard shortcut for increasing screen contrast. You can read more about this in Accessibility Programming Guide for OS X.