Thank you for your post, and I apologize for the late reply.
I am unable to replicate the problem using FileMaker Pro 11.0v3 under Mac OS X 10.6.6. Here are the steps I took.
1. I created a file with five number fields: Field1, Field2, Field3, Field4, Field5
2. I entered the same data as your example into the fields. That is, 4, 2.4, 2, 1.6 and 0.9
3. I created a bar chart (flat) and specified the five fields for the Y-axis.
4. In Browse Mode, the five values appear properly in the chart.
5. I quit FileMaker Pro, entered System Preferences -> Language & Text -> Formats -> (Numbers) Customize... and changed the Number Separators for Decimal (period to comma) and Thousands (comma to period).
6. I launched FileMaker Pro, opened the database file, and the chart still displays properly.
I am aware that a month has passed, so if you have found a solution, please post here so others can benefit. If you are still encountering the problem, please let me know what I'm doing differently than you, and I'll try to replicate the problem here.