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The 90/180 rule applies across visas. This means that your ability to use a second visa might be restricted in a way that isn't obvious from reading the visa itself.
For example, suppose you spent 80 days in the Schengen area with a 90-day visa. Two months later, you get a new 90-day visa. If your second entry is within 90 days of your previous departure, you would only be able to stay for 10 days. However, you would have 80 days remaining that you would be able to use during the latter part of the visa's validity, as long as your third entry is more than 180 days after your first.
If your visa really was a Schengen visa, though, time spent in Croatia counts separately from time spent in the Schengen area, so depending on your plans, you may be fine.