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If AMCL gives bad results, I guess the reason is poor odometry. Odometry should be continuous, i.e. it should not jump and AMCL heavily relies on it. I would generating odometry from laser scans as you mentioned in your other question a bad idea for a few reasons:

1. Odometry will jump which will cause all different kinds of problems.

2. Maybe a low frequency, depending on the frequency of your lasers. For instance, some Hokuyo lasers publish only with 10 Hz.

3. No velocity data in the Odom message. While AMCL doesn't need that, higher-level nodes such as move_base do.

Both, points 1 an 2 could cause your problems. To get a really reliable solution, I believe you will have to use real encode values for odometry.