For something like this, I would expect that it might be necessary to issue either a "clear all" or a bunch of individual clears, one for every S function used by the library, perhaps even one for every .mdl or .slx invoked. Though maybe you could use "rehash path".
When MATLAB encounters a function during execution, it parses it and caches the pre-parsed version and uses that version unless it detects at some point that a new version of the source file exists. MATLAB generally rechecks the current directory each time it returns to the command prompt, but not necessarily other directories, and sometimes it misses noticing changes. Furthermore, the pre-parsed version is where persistent variables are attached to. Sometimes it is necessary to "clear" the function or rehash to get MATLAB to drop the old parsed version.
