I received an email from SEO PowerSuite this morning concerning Market Samurai functionality, in which they say all is fine with Google, and that Market Samurai's problem isn't with Google's algorithm changes, rather problems with their software. See this from Market Samurai.
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I use both, and as Market Samurai first suggested, I also have used Raven Tools (I use that for reporting an have used it for a little over a year).
Market Samurai is a treasure full of information. I've had that tool in my back pocket for the past 3 years and love it. There are other tools on the market that do similar things, but I've never had a problem.
Probably what hurt Market Samauri most is that they use a central source to request the data from Google. PowerSuite, TrafficTravis and others all dump this on the client end of things and pretty much let us use proxies to gather information instead. That means we get CAPTCHAs, whereas before, MarketSamauri didn't have any of that either.
Most of what I do in Market Samauri I do in RavenTools. The RankTracker in SEO Powersuite is a mess. It's nice for small sites, but when I'm doing a report on my own site with just over 2000 terms and looking for the top 500 results, it takes more than 16 hours to complete the report. Just awful. RavenTools I get thousands of keywords for multiple sites, and the report comes out once per week without issue.
I'm not a fan that MarketSamauri is going to change to a monthly payment module. PowerSuite already has a monthly fee that they charge for data too (although they kinda sneak that in on you after the fact). Between my various tracking tools, and monthly fees, I'll probably still continue using it.
I do love the update that was made by SEO Powersuite to their Website Auditor. Much nicer interface, and now allows saving of PDF files - longtime request finally honored.
The only issue that I have so far is that Market Samauri says there was an Algo change, yet nobody else has confirmed this. We'll have to wait and see how it unfolds I guess.