I bought an Ibanez s521 off Ebay advertised as a factory 2nd, and the condition appears perfect, no blemishes or anything. This is a fixed bridge with no trem.

However, the guitar appears to be every so slightly out of tune at certain frets, hence if I tune it as you normally would on the 5th fret, and then doing a regular D-Chord, then say moving while holding the D-chord formation across the fretboard (say to 5th to 7th to 12th), I can hear a slight twang that shouldn't be there.

The issue is pretty slight, so I guess I can live with it, but was wondering if anyone has any ideas. I guess the obvious is to change the strings first.

I checked the intonation by comparing the 12th fretted note to the harmonic, and didn't find a problem.

Overall, I'm a bit dissapointed in the Ibanez s521. I had an older Ibanez from the early to mid 1990's (not sure what model), and it was just a MUCH better guitar than this s521. Not only was the older Ibanez easier to play, but the harmonics and pickups were so much better. I guess they put crappier or cheaper pickups in them these days. I probably should have played one at the Guitar Store before buying it, but I was just expecting it to play similarly to my old Ibanez (but nope, so sad)... I read so many great things about the Ibanez S-series, and maybe the ones with floating bridges are better, but very very dissapotined in the s521.

I guess because this is a fixed bridge, the s521 plays more like a Fender Strat than an Ibanez and has very tout tension. I haven't tried slinkier strings yet though or thinner gauge.
I had a late 90s 540s that was an awesome guitar. One of the easiest playing guitars I have ever owned. I am an Ibanez fan, but I have I tried several S series new at my local GC, and they don't even compare to my old model. Not close.

As for your problem, if the intonation is good I have no clue what it could be. Sorry I couldn't be of more help, but good luck.
Yah this Ibanez s521 plays like a low-priced strat other than it does have a decent neck, though once I get some slinkier strings we will see if that helps. Unfortunately I don't think the Ebay seller will take the guitar back.

I also preferred my old Ibanez neck overall, but this one has an ok neck. My old Ibanez had incredible pickups for both clean and distorted, these pickups on this one are truly some of the worst I've ever heard on a $400+ guitar, OH MY they are horrible.

I mean the s521 is $399 new, so it's not like a super super cheap guitar, but I am regretting the purchase and wish I had just gone to the Guitar Store and ponied up $1000 for whatever guitar I found to be best.

Now I will have to sell this one and buy a different guitar eventually.