They are fully identical.
No, the 0.9.8 file the drill section starts with <drill>, the drill section in 1.0 file starts with <drill Enabled="true">.
Also the order of the values is different.
This has nothing to do with this message but if the files are identical for you there is a mistake.
The message you get means that you have a different default value in your 0.9.8 version then in the 1.0.
You have to look at the styles in your versions. Start with changing the value for "Drilling Method" to standard in the CAM style "without name" in both versions. If you set both to "standard" you don´t get the message.
It is only a message and no error.
The message tells you that the basic settings in your versions are different. I mean this is not a bug.