Emmanuelle,
are you sure, you were running on your server system tclsh and aolserver with the same environment variables and linked against the same tcl shared libs? I see with both, Mac OS X and lenny/sid with aolserver 4.5.1 and 4.0 in tclsh and ds/shell always utf-8 for [encoding system].
background: During initialization, Tcl determines the default system encoding from the LC_* or LANG environment variables. If nothing can be found, it uses TCL_DEFAULT_ENCODING, which is set depending on the OS. For example, under Mac OS X the TCL_DEFAULT_ENCODING is utf-8. If configure can't determine anything, the final default system encoding is "iso8859-1". Later, Tcl's system encoding can be altered on the scripting layer via "encoding system ?XXX?" or from C via Tcl_SetSystemEncoding(). Aolserver 4.0.10/4.5.1 does not set it via Tcl or C, naviserver has a config variable named "systemencoding" and sets the encoding in init.tcl (if nothing specified, it defaults to utf-8).
note, that when you load a library file or a www/*tcl script that sets the encoding via "encoding system ...", it is set for the whole server (all threads). The system encoding is a global variable in the Tcl implementation. The only OpenACS package that sets the system encoding is lors-central (most likely, not a good idea).
It is a good idea to check the LANG variable in your startup script for aolserver and use in doubt something like LANG=en_US.UTF-8
Hope this helps and all the best
-gustaf neumann