Enchanced fix. Again, rename the original "/usr/bin/yelp" to something else, e.g. "/usr/bin/yelp.orig" (you need to install the yelp package first), and then create a new /usr/bin/yelp file with this content:
#!/bin/sh
xmodmap -e 'keysym 0x31 = 1 exclam'
xmodmap -e 'keysym 0x34 = 4 dollar'
xmodmap -e 'keysym 0x39 = 9 parenright'
Save and then do "chmod 755 /usr/bin/yelp".
After opening gnome applications, like gnumeric and epiphany browser, press [1] once. This should make [1], [4], [9] produce "1", "4" and "9", and Shift [1], [4], [9] to produce "!", "$", ")" respectively. i.e. the normal behavior.
I have just tested the number keys [1]-[0], all keys are working with the right symbols with [Shift].
Please test to see if any other key are misbehaving. I will then make/include this into a new scriptpack and let users just run a simple "./install.sh" to fix this.