You don't really give us many details. I don't know anything about the FIDE online arena software, and you didn't mention the name of the other program you used.
Do the two programs analyze each move for the same period of time? Do the two programs run Stockfish using the same number of threads? Do they use the same hashtable size?
(Not knowing any more than I already know, I'd tend to assume that the FIDE program is wrong; I just assume that anything FIDE touches will get screwed up. 
)
Depends on how the engine is set up. You know, how far ahead it's looking and whatever other parameters are tweaked by the GUI. Couple years ago someone was furious that his software wasn't performing to his expectations and made a thread. So I'm just parroting what some computer guy said to him back then, but it does kind of make sense when you think about it. Just like how well an engine performs depends on what car it's installed in, what the gearing is, and how much the car weighs. Sorry for the analog explanation in a digital world, but it's the best I can do. 
Unless you are 100% sure that you are running the exact same engine version, using the same parameters, on the same hardware...you have no cause for complaining that results do not match.
And whatever this FIDE Online Arena application is, it requires Java to run.
Be afraid...Be very afraid.
Annnnnd, SSL Labs gives their secure server an "F" rating. 
https://www.ssllabs.com/ssltest/analyze.html?d=arena.myfide.net
SMP searches are non-deterministic. So unless you analyze on a single core/thread or a position that that resolves into a forced mate, there are bound to be variations in the moves and evals.
@escher..i click move in the first program and it shows vars then i click on 2nd program and it shows vars so i do not click at same second in both programs. Fide software from arena.myfide.net where i only just set depth to 10, the other is free chessbase reader soft where i do not see any setting for stockfish so it is using default settings i guess. Both these softs is using same stockfish program saved in my comp.
@escher..i click move in the first program and it shows vars then i click on 2nd program and it shows vars so i do not click at same second in both programs. Fide software from arena.myfide.net where i only just set depth to 10, the other is free chessbase reader soft where i do not see any setting for stockfish so it is using default settings i guess. Both these softs is using same stockfish program saved in my comp.
OK, I'm not surprised that you get different answers for the two programs. The engine version is the only thing that we know is the same; Everything else very well could be different. In the FIDE program, it's analyzing to a fixed depth, while you're manually turning the engine on and off in the other program. Also, it is very possible that the engine settings are different. Finally, what Nebber_Agin said could also be a factor.
Unless you are 100% sure that you are running the exact same engine version, using the same parameters, on the same hardware...you have no cause for complaining that results do not match.
Can somebody just state "i thought for same game stockfish analysis variations per move would match in any software" without it being branded "complaining". This isn't your typical "my opponent won't resign thread"
Hiii
To analyze my finished games i am using fide online arena software and another software downloaded from web. in both of these softwares i installed stockfish engine to show various lines per move to ease analysis. But stockfish showing different variations per move in both of these softwares on same game, means variations do not match! or matches only sometimes but not all moves in the variation, i thought for same game stockfish analysis variations per move would match in any software. Why is the problem?