I think the problem is that you are mixing xmodmap commands with setxkbmap commands (whether on the command-line or by using the graphical settings menus). As you have observed, the setxkbmap commands will override the xmodmap commands when you change your keyboard layout. The logical solution would therefore be to use setxkbmap to change both your layout and the keypad comma to a decimal period.

When you use setxkbmap to change your layout any specified customisations will also be applied: the full list of options is available at /usr/share/X11/xkb/rules/evdev.lst. I don't know which language layouts you use, so I have placed just two examples at the end of the following command, which you can use to switch layouts with ALt+Shift. If you have any more key mappings or bindings you want to activate, simply add them to the command:

setxkbmap -option '' -option kpdl:dot -option grp:switch,grp:alt_shift_toggle gb,nl

The first command switch (-option '') clears any current settings, as when new settings are given they are added to and do not replace any existing ones unless this option is used. The second (-option kpdl:dot) makes sure that the appropriate keypad key is a dot or period; the third command switch (-option grp:switch,grp:alt_shift_toggle) sets up your ability to switch the layouts with ALt+Shift, and the last (gb,nl) specifies the layouts to switch to.

To check your settings, you can enter

setxkbmap -query

which results in:

rules:      evdev

model:      pc105

layout:     gb,nl

options:    kpdl:dot,grp:switch,grp:alt_shift_toggle

Add the full setxkbmap line further above as a startup item to make sure it is activated and available for you to use.

More information on setxkbmap is available by entering man setxkbmap or by viewing the Ubuntu manpages online.