Yes and sadly no one can fix this.Maybe its just a bearing noise but they say opening it makes it worst. I noticed most manual gears got some noise I Was surprised to see our office car that is 50k driven had gear noise in first or 2nd gear. Putting qabli gear its a brack breaking work than no gurantee of silent one. I kno some one who changed 7 gears to get a noiseless one than he settled for 7th noisy one
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BTW I like C52 transmission, It pulls better, Shifts better and much better than C51 of 5AFE. In fact I feel its kinda easier to drive and Might be giving better mileage. But why Toyota opted for short gear Transmission like C52 for a engine that has ample low end torque and mounted C51 to an engine (5AFE) that has comparatively weak torque.
I told one of the old engine dealer in Pindi to get me 7AFE gear he was like aik he hota hai when I told him he was surprised and than there no clear way to determine which one you are getting they both look identical and no model no on them.