Let's start off with recognizing one basic fact. The REAL behavior of concrete is non-linear. Cracking, and creep for material non-linearity. And, then our regular P-Delta and p-little delta for geometric non-linearity.
For analysis, we typically take the material non-linearity out of it by assuming 0.7*Igross for columns and 0.35*Igross for beams. That's the standard way that most engineers account for cracking so that they can ignore (or greatly simplify) material non-linearity. We all know it's a gross over simplification, but that's what we do because it we're engineers not PhD researchers.
Chapter 6.6 Elastic First Order Analysis
When I mentioned the 0.25EI, that was referring to the Chapter 6.6 (of ACI 318-2014). Specifically, the P-little delta amplification factor..... Cm/{1-Pu/(0.75*Pc)}
Where Pc really equals the "euler buckling" load:
Pc = Pe = pi^2 * EI_eff / (KL)^2
In ACI 2014 (and going back a number of code cycles), EI_eff (for the purpose of the p-little delta amplification) can be estimated by section 6.6.4.4.4 (reference from ACI 318-2014).
The first equation given is 0.4*E*Igross / (1+Beta_dns)
Beta_dns is the ratio of maximum sustained factored load to maximum factored load. In the commentary they suggest Beta_dns can be assumed to be 0.6, which makes EI_eff = 0.25 EI gross. But, only for the purpose of this moment amplification equation.
Why do they use such a smaller value for this? To account for creep caused by sustained loads and the effect it could have on very slender columns.
Personally, I'm not a big fan of this type of amplification. This is all based on the assumption that you performed an Elastic - First Order analysis. Meaning, no material nonlinearity (I = 0.7 or 0.35) and no geometric non-linearity (i.e. hand calc methods for P-Big Delta and P-Little Delta).
Chapter 6.7 Elastic Second Order Analysis:
Now, Chapter 6.7 more accurately captures what I really think engineers are doing. The rest of the world (or the academics) would call this GNA (Geometrically non-linear analysis), which means we're accounting for the non-linearity due the change in geometry of the structure. P-Delta and P-little delta.
Rather than mess around with all the funny hand methods for amplification, section 6.7.1.2 (and the commentary) suggest that you capture P-little delta if you merely sub-divide your columns between floor levels. But, that means, their P-little delta amplification is now based on whatever assumptions you used for Icracked.... usually 0.7 Igross.
Hence you have a MAJOR difference between how p-little delta effects are calculated between the two methods of analysis. But, both methods still follow the letter of the code. Now, when is this a big deal?
Only when column slenderness is significant. I don't have a great feel for this for concrete (as most of my stability work has been with steel). But, the KL/r > 22 is a trigger for sway frames and KL/r > 40 is a trigger for non-sway frames.
Personally, I usually start my analysis WITHOUT sub-dividing my columns. When I'm close to a finalized design, then I'll sub-divide the most slender of them. If their moments change by more than 1% then I'd probably sub-divide them all and see how much of a change I get. If it's consistently above 1% difference from the moments before subdivision, then I would take a closer look at the P-little delta effect by hand rather than purely relying on the computer programs P-Delta analysis.