Hi, I use pd (ext) since several years, and first of all, congratulation and thanks for this great project! Here are some bugs and problems I experienced. I run PD on Ubuntu Oneiric, and also tried it on another computer on Maverick... These bugs are present in the download from april 11th.
* the text around vu-meters is covered by them. (I run pd in french,
  maybe it has something to do: 'entrées' 'sorties' (in, out) ).
* Settings save: I understand now why it isn't possible to save
  paths/libs anymore, but I also cannot save other settings, like
  edit modes, or verbose level...
* On Maverick, déjà-vu sans mono is not found, but installed on the
  system...
* There is a bug with [knob] Gui object: when editing preferences,
  and then apply or 'ok', nothing happens and pref windows is
  stuck... Have to close pd and reopen, then the changes are
  effective. Here is the log:
(Tcl) ERREUR NON GÃRÃE : expected integer but got "Sans" (processing "-font" option) invoked from within ".x9ae7ae0.c itemconfigure 9ae1a48LABEL -font {DejaVu Sans Mono 8 bold} -fill #000000 -text {} " ("uplevel" body line 1) invoked from within "uplevel #0 $cmds_from_pd"(Tcl) ERREUR NON GÃRÃE : expected integer but got "Sans" (processing "-font" option) invoked from within ".x9ae7ae0.c itemconfigure 9ae1a48LABEL -font {DejaVu Sans Mono 8 bold} -fill #000000 -text {} " ("uplevel" body line 1) invoked from within "uplevel #0 $cmds_from_pd"
* Then, there is a big point, that have been already discussed many
  times: autoconnect sound/midi in jack should really be disabled,
  or made it possible to choose. Midi autoconnects with all clients,
  and we have to 'disconnect all' before patching as desired. Same
  with sound: sometimes, I use pd to make sound in a basic way, and
  just output on channels 1 - 2, but most of the time, I use it as a
  plugin, or inserted between several other jack-applications, with
  particular jack patches. The patchbay from qjackctl save my
  desired connection, and I should only start my apps and let the
  connections make themselves. The patch is the power of jack, and
  autoconnect goes against this philosophy. Also, maybe one day pd
  will be compatible with ladish/jack-session (the future of jack!).
* Of course, I didn't tested everything, but most of my old patches
  seems to work on 0.43.1...
hope this will be helpful... r