SYMPTOM:
Conditional Formatting option allows users to change the display of value in each row depending on the metric value. For general instruction for how this feature works, please refer to:KB11941: How to use conditional formatting thresholds on individual report objects in a MicroStrategy Report Services 8.x and 9.x document
Note: Graphic User Interface in version 9.0.x has changed. However, the explanation for each option is valid to version 9.0.x.
Suppose conditional formatting is specified as follows:

However, when the report is executed, 0 appears as 0, not as 0.00.

CAUSE:
The is working as designed, since the Replace Text threshold was designed to change numbers into strings. Even though numbers are entered there, they are treated as strings.
ACTION:
Manually specify decimal points like "0.00."
For more information about related topic, please refer to:
KB18591: ‘Replace Text’ option in thresholds will cause exported cells in Microsoft Excel appear formatted as text even when the replaced text is a number in Microstrategy Desktop and Web 8.1.x