Had the same problem with LMDE Xfce 64.
As I understand it, Update 4 updates the Boinc manager version and it now seems to now takes the setting instructions from the website whereas the old version took it's settings from the local .cfg file.
I went to my account on the Boinc project I am running website and made all the relevant settings and saved.
On Boinc Manager - Opened, 'View', 'Advanced View', Project, and clicked on the Update button and it downloaded the settings and started working.
I have another installation of LMDE Xfce 64 with Boinc which refuses to allow a project to be installed. I have completely uninstalled it a few times before realising that Synaptic Complete Uninstall doesn't actually fully uninstall it and leaves some settings behind. When I have time I must fully delete all traces of it, re-install and then hopefully it will run. One thing I have noticed is that the same Boinc project, on the same hardware, with the same settings produces far better results on Ubuntu 12.04 than with LMDE Xfce.
CPU = U9300, 4GB RAM, Intel GM45 Graphics @ resolution 1366x768, 128GB internal drive, 6TB external storage, Main OS = LMDE Xfce 64bit UP4. 2nd OS = LMDE Xfce 64bit UP4, Other installed OSs = Bodhi 1.4.0, Ubuntu 10.04 & 12.04, Mandriva & Windows.