How to disable transpose shortcut

One possible reason is that your user account has lost rights to change services preferences file (some buggy installers can cause that). Open Terminal and type

ls -la ~/Library/Preferences/pbs.plist

If you see that the owner is root, that is the problem:

-rw-------    1 root  wheel    1407 Jan 16 13:40 /Users/me/Library/Preferences/pbs.plist
                  ↑
                 incorrect!

In that case, you can fix the problem by typing this command (replace me with your user name; you will be asked for your password):

sudo chown me:staff ~/Library/Preferences/pbs.plist

To change the shortcut of a service, run plutil -convert xml1 ~/Library/Preferences/pbs.plist, open the plist, and change for example

<key>(null) - Some Service - runWorkflowAsService</key>
<dict>
    <key>key_equivalent</key>
    <string>@~a</string>
</dict>

to

<key>(null) - Some Service - runWorkflowAsService</key>
<dict>
    <key>key_equivalent</key>
    <string>@~&#x8;</string>
</dict>

Then restart to apply the changes.

@ is command, ~ is option, and  is delete (Windows backspace). Forward delete (Windows delete) would be . The shortcut strings use the same format as in DefaultKeyBinding.dict.

To change a global shortcut set in the App Shortcuts section, run plutil -convert xml1 ~/Library/Preferences/.GlobalPreferences.plist, open the plist, and change for example

<key>Some Menu Name</key>
<string>~@a</string>

to

<key>Some Menu Name</key>
<string>~@&#x8;</string>

Then quit and reopen applications to apply the changes.

Application-specific shortcuts are stored in ~/Library/Preferences/*.plist and ~/Library/Containers/*/Data/Library/Preferences/*.plist.