Interlayer interactions play an important role in the formation of two-dimensional covalent organic frameworks (2D COFs), yet the effects of monomer structure on COF formation, crystallinity, and susceptibility to exfoliation are not well understood. Here we probe these effects by studying the stacking behavior of imine-linked macrocycles that represent discrete models of 2D COFs. Specifically, macrocycles based on terephthaldehyde (PDA) or 2,5-dimethoxyterephthaldehyde (DMPDA) stack upon cooling molecularly dissolved solutions. Both macrocycles assemble cooperatively with similar ΔH e values of -97 kJ/mol and -101 kJ/mol, respectively, although the DMPDA macrocycle assembly process showed a more straightforward temperature dependence. Density functional theory calculations of the stacking of PDA macrocycles suggested two stable configurations that were close in energy. Circular dichroism spectroscopy performed on macrocycles bearing chiral side chains revealed a helix reversion process for the PDA macrocycles that was not observed for the DMPDA macrocycles. Given the structural similarity of these monomers, these findings demonstrate that the stacking processes associated with nanotubes derived from these macrocycles, as well as for the corresponding COFs, are complex and susceptible to kinetic traps, casting doubt on the relevance of thermodynamic arguments for improving materials quality. Rather, a deeper understanding of the mechanism of supramolecular polymerization and its interplay with polymerization and error correction during COF synthesis is needed for improved control of the crystallinity and morphology of these emerging materials.