Please try via apt-get update and post the logs...
N900:~# apt-get update Hit http://maemo.merlin1991.at fremantle Release.gpg Ign http://maemo.merlin1991.at fremantle/free Translation-en_GB Ign http://maemo.merlin1991.at fremantle/non-free Translation-en_GB Get:1 https://downloads.maemo.nokia.com ./ Release.gpg [198B] Get:2 http://skeiron.org fremantle Release.gpg [3B] Get:3 http://skeiron.org fremantle/free Translation-en_GB [3B] Get:4 http://skeiron.org fremantle Release.gpg [3B] Get:5 http://skeiron.org fremantle/free Translation-en_GB [3B] bzip2: (stdin) is not a bzip2 file. Ign http://skeiron.org fremantle/free Translation-en_GB Get:6 http://skeiron.org fremantle Release.gpg [3B] Get:7 http://skeiron.org fremantle/free Translation-en_GB [3B] Ign https://downloads.maemo.nokia.com ./ Translation-en_GB 94% [5 Translation-en_GB bzip2 0] [Connecting to maemo.merlin1991.at]bzip2: (stdin) is not a bzip2 file. Ign http://skeiron.org fremantle/free Translation-en_GB 93% [7 Translation-en_GB bzip2 0] [Connecting to maemo.merlin1991.at (188.40.39bzip2: (stdin) is not a bzip2 file. Ign http://skeiron.org fremantle/free Translation-en_GB Hit http://maemo.merlin1991.at fremantle Release Hit http://skeiron.org fremantle Release Get:8 https://downloads.maemo.nokia.com ./ Release.gpg [198B] Hit http://skeiron.org fremantle Release Ign https://downloads.maemo.nokia.com ./ Translation-en_GB Hit http://skeiron.org fremantle Release Ign http://maemo.merlin1991.at fremantle/free Packages/DiffIndex Ign http://maemo.merlin1991.at fremantle/non-free Packages/DiffIndex Get:9 https://downloads.maemo.nokia.com ./ Release.gpg [198B] Get:10 http://skeiron.org fremantle Release [3B] Ign http://skeiron.org fremantle Release Get:11 http://skeiron.org fremantle Release [3B] Get:12 http://skeiron.org fremantle Release [3B] Ign http://skeiron.org fremantle Release Ign http://skeiron.org fremantle Release Ign http://maemo.merlin1991.at fremantle/free Packages Ign https://downloads.maemo.nokia.com ./ Translation-en_GB Ign http://maemo.merlin1991.at fremantle/non-free Packages Get:13 http://skeiron.org fremantle/free Packages [3B] 97% [13 Packages bzip2 0] [Waiting for headers] 34B/s 0sbzip2: (stdin) is not a bzip2 file. Err http://skeiron.org fremantle/free Packages Sub-process bzip2 returned an error code (2) Hit https://downloads.maemo.nokia.com ./ Release Get:14 http://skeiron.org fremantle/free Packages [3B] Get:15 http://skeiron.org fremantle/free Packages [3B] 97% [Release gpgv 507] [14 Packages bzip2 0] [Connecting to maemo.merlin1991.atbzip2: (stdin) is not a bzip2 file. Err http://skeiron.org fremantle/free Packages Sub-process bzip2 returned an error code (2) 97% [Release gpgv 507] [15 Packages bzip2 0] [Connecting to maemo.merlin1991.atbzip2: (stdin) is not a bzip2 file. Hit https://downloads.maemo.nokia.com ./ Release Err http://skeiron.org fremantle/free Packages Sub-process bzip2 returned an error code (2) Hit http://maemo.merlin1991.at fremantle/free Packages Hit https://downloads.maemo.nokia.com ./ Release Get:16 https://downloads.maemo.nokia.com ./ Release [507B] Hit http://maemo.merlin1991.at fremantle/non-free Packages Get:17 https://downloads.maemo.nokia.com ./ Release [507B] Ign https://downloads.maemo.nokia.com ./ Release Get:18 https://downloads.maemo.nokia.com ./ Release [507B] Ign https://downloads.maemo.nokia.com ./ Release Ign https://downloads.maemo.nokia.com ./ Release Ign https://downloads.maemo.nokia.com ./ Packages/DiffIndex Ign https://downloads.maemo.nokia.com ./ Packages/DiffIndex Ign https://downloads.maemo.nokia.com ./ Packages/DiffIndex Ign https://downloads.maemo.nokia.com ./ Packages Ign https://downloads.maemo.nokia.com ./ Packages Ign https://downloads.maemo.nokia.com ./ Packages Hit https://downloads.maemo.nokia.com ./ Packages Hit https://downloads.maemo.nokia.com ./ Packages Hit https://downloads.maemo.nokia.com ./ Packages Fetched 2151B in 11s (183B/s) W: GPG error: http://skeiron.org fremantle Release: The following signatures were invalid: NODATA 1 NODATA 2 W: GPG error: http://skeiron.org fremantle Release: The following signatures were invalid: NODATA 1 NODATA 2 W: GPG error: http://skeiron.org fremantle Release: The following signatures were invalid: NODATA 1 NODATA 2 W: GPG error: https://downloads.maemo.nokia.com ./ Release: The following signatures were invalid: KEYEXPIRED 1349249546 KEYEXPIRED 1349249546 KEYEXPIRED 1349249546 W: GPG error: https://downloads.maemo.nokia.com ./ Release: The following signatures were invalid: KEYEXPIRED 1349249546 KEYEXPIRED 1349249546 KEYEXPIRED 1349249546 W: GPG error: https://downloads.maemo.nokia.com ./ Release: The following signatures were invalid: KEYEXPIRED 1349249546 KEYEXPIRED 1349249546 KEYEXPIRED 1349249546 W: Failed to fetch http://skeiron.org/repository.maemo.org/community/dists/fremantle/free/binary-armel/Packages.bz2 Sub-process bzip2 returned an error code (2) W: Failed to fetch http://skeiron.org/repository.maemo.org/extras/dists/fremantle/free/binary-armel/Packages.bz2 Sub-process bzip2 returned an error code (2) W: Failed to fetch http://skeiron.org/repository.maemo.org/extras-devel/dists/fremantle/free/binary-armel/Packages.bz2 Sub-process bzip2 returned an error code (2) E: Some index files failed to download, they have been ignored, or old ones used instead. N900:~#
N900:~# cat /etc/apt/sources.list.d/hildon-application-manager.list deb http://maemo.merlin1991.at/cssu/community-thumb/ fremantle free non-free deb https://downloads.maemo.nokia.com/fremantle/ssu/apps/ ./ deb https://downloads.maemo.nokia.com/fremantle1.2/ovi/ ./ deb https://downloads.maemo.nokia.com/fremantle/apps/ ./ deb http://skeiron.org/repository.maemo.org/community/ fremantle free deb http://skeiron.org/repository.maemo.org/extras/ fremantle free deb http://skeiron.org/repository.maemo.org/extras-devel/ fremantle free N900:~#
Do NOT edit the HAM sources list manually but edit Application Catalogues using HAM.