Clearly you are working with slow growing bacteria.
Has the variation been observed between parallel cultures of the same isolate, in the same medium, at the same incubation temperature, pO2, pC02 and so on?
How do you monitor growth? Do you estimate doubing time in the log phase?
If you wish, send me an excel sheet with all the raw experimental points of one of the experiments that worry you, An ANOVA analysis might clarify the situation.