I have found a solution.
The key is to redefine the "run" command.
In CodeBlocks, under Project -> Properties -> Debugger -> Debug -> Additional commands, in the box "Before connection" put the following:
source fixrun
target palmos
The new line is "source fixrun".
Then, in the main directory of the project, create a textfile called "fixrun" which contains the following:
define run
cont
end
That is it!
When you start the debugger, it will run the "Before connection" commands. The "Source" command reads in a command file. The "define" command redefines "run" as "cont", so that if a "run" command is issued, it is translated to a "cont". This has to be in an external file, since otherwise there is an interactive dialog which asks if your really want to replace the command "run".
Now, continuing, and breakpoints work as they are supposed to. Run to cursor, however is still broken.