Issue: When comparing NCM configs for same device (Running / Startup / Baseline) device showing blank lines
(Two blank lines marked as difference )

Troubleshooting :
Please check on the device configuration what are they through Putty / Telnet
for example Sh run through putty ? see what values are there ?
Blank lines ?

Cause:
That's basically device behavior these lines are not blank
There are some characters even device is failed to show these characters therefor NCM failed as well and we cannot create Regular expression to ignore.
Resolution:
NCM cannot ignore this unless we know what to ignore. Please check with Vendor if these can be removed from the device config.
Expected behavior from NCM comparing the config line by line and then providing information if there is something not matching exactly .
Work around may work
You can also try some carriage return regex if this helped in your case however it depends on device to device.
For Carriage return try below
(\n\r\f)
For more details please see below posts
Explanation:
NCM compares the configuration line by line and if there is any mis-match violations in the compared configuration it will be notified .
NCM cannot compare a specified config block and ignore the rest of the config the functionality will check and compare the complete configuration compared and any violations will be notified any line can be ignored using creating regex Comparison criteria under NCM.
Regular expression / Config Comparison issues - Ignore Blank Lines
How do I ignore lines in downloaded configs when comparing in NCM
Cirrus Regex pattern for ignoring blank lines with whitespaces
Help with regular expressions and config change reports
NCM Compliance Rule RegEx at the end of the line
Regular expression pattern matching examples
Exclude config content from comparison in NCM
Conflict: Running configs and startup configs do not match