Here is alternate guarding from the KOF2002 wiki here:
"Alternate Guard: This is a glitch that is very useful for avoiding throws. The way it works is that if the opponent has done some kind of move that has put you into a blocking animation, then you can keep that blocking animation going indefinitely by quickly alternating crouch block with stand block. Whlie you are alternating, all throws that the opponent attempts will miss, including one frame command throws(Daimon hcb f+P), delayed command throws(O Yashiro hcf+P and qcb+P, Clark dp+K), Daimon's autoguard hcfx2+K, proximity throws such as Andy hcf+P and O Chris hcf+K and normal f+C/D throws.
Blocking animation is triggered if you are holding back while a blockable move is executed by the opponent. That move does not actually have to be blocked by you in order for the block animation to be triggered.
A basic and dangerous tactic that a grappler could do to you is to throw you after landing from a jump attack, or to do a weak attack into a throw. Without alternate guard, avoiding this after you have blocked the jump attack or the weak attack, requires you to jump(or throw him first which may or may not work out). The problem is that a jump has startup vulnerability frames in which your character can get hit before he actually lifts off the ground. If the grappler decides to instead do a close C after his jump attack or weak attack, you would get hit by it if you attempted to jump out expecting a throw.
Alternate guard allows you to avoid the throw and to block the close C without the risk of guessing wrong. Alternate guard makes you vulnerable to high and low attacks, depending on your block position when a move makes contact. Jump attacks are generally not much of a threat against alternate guard because it is easy to see when someone jumps, but many fast low attacks are generally impossible to react to...which means, if you are alternating high/low with equal speeds, you have a 50% chance to get hit with a low attack.
To minimize the risk of getting hit low, it's important to know that you don't really have to alternate at the same speeds...I'm not sure of the exact frames but you can alternate for say, one frame high and 5 frames low, and will keep you vulnerable low only 1/6th the time. "http://dreamcancel.com/wiki/index.php?title=King_of_Fighters_2002#Practical_Tricks_.26_GlitchesAlso, a good thing to know is the different kinds of throws. As mentioned above, there are:
1.) 1 instant framers (Clark's hcf+K, Vice's hcb, f + P, Orochi Yashiro's hcb, f + P etc.)
2.) Delayed throws (Clark's dp+k, Chris's dp+P, Daimon's dp + P etc.)
3.) Proximity unblockables (98 Robert's hcf + K, 02UM King's hcf + P, normal throws)
4.) blockable throws (Hinako's hcf + k)
But yeah, good players that play with grapple characters can be a nightmare sometimes. Just keep at it, and try to understand and remember when they whip out their throws the most under what situations.